Pseudobulk TE Heatmap Visualization

Overview

This notebook provides a complete workflow to generate pseudobulk heatmaps for transposable element (TE) and HERV expression in single-nucleus RNA-seq data from the ASAP PMDBS cohort. It includes functions to read and merge count matrices across brain regions, normalize counts by pseudobulk nuclei, and cluster both columns (pseudobulks) and rows (TEs) based on metadata or TE annotation. The workflow supports flexible filtering, annotation, and ordering of samples and TEs, enabling detailed visualization of TE expression patterns across cell types, brain regions, and disease status. The resulting heatmaps highlight expression trends and facilitate comparison with bulk RNA-seq measurements.

Key features include:

• Reading TE and HERV count matrices for single or multiple brain regions.
• Clustering columns (pseudobulks) by metadata (cell type, region, diagnosis, etc.).
• Clustering rows (TEs) by annotation groups (e.g., TE subfamily) or expression patterns.
• Normalization by number of nuclei per pseudobulk.
• Optionally returning the normalized data without generating the heatmap.
• Flexibility to filter low-abundance pseudobulks or select specific TE subsets.

1. Load required libraries

# Loading libraries
library(data.table)
library(ggplot2)
library(pheatmap)
library(RColorBrewer)
library(ggpubr)
library(openxlsx)
library(tidyverse)

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library(stringr)

2. TE count data import functions

2.1 Read TE counts for a single region

Purpose:

Reads TEs count matrices for a single brain region, across clusters. Returns a list containing: * te_counts: count matrix (TEs x pseudobulks). * samplesheet: metadata for each pseudobulk column.

Notes:

• Supports both RepeatMasker (TE_) and RetroTector (HERV) prefixes.
• Merges matrices from multiple clusters for the same region.

# Read files of a single brain region of the cohort
# Returns a count matrix and a samplesheet for it
read_te_counts_asap_region <- function(region, prefix=NA){
  # Read the complete samplesheet
  samplesheet <- read.xlsx("/Volumes/MyPassport/ASAP/code/ASAP_PMDBS_snRNAseq/original/ASAP_samplesheet.xlsx")
  clusters <- as.character(0:7)
  # For each of cluster
  for(cluster in clusters){
    print(cluster)
    print(region)
    # TE is the prefix for reading the TE count matrices from the repeatmasker quantification
    # HERV is the prefix for reading the count matrices from the retrotector quantification
    if(is.na(prefix)){
      prefix = "TE_"
    }else{
      prefix = prefix
    }
    # If it is the first iteration, we create the matrix (te_counts)
    if(cluster == "0"){
      te_counts <- fread(paste("~/inbox/ASAP/trusTEr_output_vs2/",region  ,"/", prefix, "_counts_", region, "_", cluster, ".csv", sep=""), sep = ",", data.table = F)
      # Geneid is the TE id
      rownames(te_counts) <- te_counts$Geneid
      # Subset the samplesheet for the brain region of interest
      samplesheet_list_clusters <- samplesheet[which(samplesheet$Region == region),]
      rownames(samplesheet_list_clusters) <- paste(rownames(samplesheet_list_clusters), "_", cluster, sep="")
      # If we would keep using samplesheet, we would have one entry per sample, but it would be convenient to have one entry per pseudobulk (per column of the heatmap), so, we add a column with the cluster number and the next iteration we bind the rows
      samplesheet_list_clusters$cluster <- cluster  
    }else{
      # If it's not the first iteration, we can just cbind or merge to the existing te_counts
      # Read
      tmp <- fread(paste("~/inbox/ASAP/trusTEr_output_vs2/",region  ,"/", prefix, "_counts_", region, "_", cluster, ".csv", sep=""), sep = ",", data.table = F)
      # If they are sorted exactly the same way, it is safe to cbind
      if(all(te_counts$Geneid == tmp$Geneid)){
        te_counts <- cbind(te_counts, tmp[,7:ncol(tmp)])
        # Otherwise we merge by TE id (significantly slower)
      }else{
        te_counts <- merge(te_counts, tmp[,c(1, 7:ncol(tmp))], by="Geneid")
      }
      rownames(te_counts) <- te_counts$Geneid
      # We subset samplesheet
      tmp_samplesheet <- samplesheet[which(samplesheet$Region == region),]
      rownames(tmp_samplesheet) <- paste(rownames(tmp_samplesheet), "_", cluster, sep="")
      # Add cluster number
      tmp_samplesheet$cluster <- cluster  
      # And bind to the existing (increasing) samplesheet_list_clusters
      samplesheet_list_clusters <- rbind(samplesheet_list_clusters, tmp_samplesheet)
    }
  }
  # We return a list of the count matrix and its respective samplesheet (one row per column in te_counts)
  return(list("te_counts" = te_counts, "samplesheet" = samplesheet_list_clusters))
}

2.2 Read TE counts accross multiple regions

Purpose:

Reads TE or HERV count matrices for a single brain region, across clusters. Returns a list containing: * te_counts: count matrix (TEs x pseudobulks). * samplesheet: metadata for each pseudobulk column.

Notes:

• Supports both RepeatMasker (TE_) and RetroTector (HERV) prefixes.
• Merges matrices from multiple clusters for the same region.

# We have 4 brain regions in this cohort, so it is convenient to have a wrapper to call read_te_counts_asap_region() for each of the regions
# It inputs a vector of the regions of interest and the prefix for the matrix reading
read_te_counts_asap_multiregion <- function(regions, prefix=NA){
  if(length(nchar(regions)) > 1){
    print("More than one region")
    # For each of the regions
    for(r in 1:length(regions)){
      print(paste("Region", regions[r]))
      # If it is the first iteration, we can read and create the te_counts matrix were all the results will end up in
      if(r == 1){
        tmp <- read_te_counts_asap_region(regions[r], prefix=prefix)  
        te_counts <- tmp$te_counts
        # And its samplesheet of course.
        samplesheet <- tmp$samplesheet
        rm(tmp)
      }else{
        # If it is not the first iteration, we can just check that it is ordered the same way and cbind or merge if needed 
        tmp <- read_te_counts_asap_region(region = regions[r], prefix = prefix)  
        if(all(te_counts$Geneid == tmp$te_counts$Geneid)){
          te_counts <- cbind(te_counts, tmp$te_counts[,7:ncol(tmp$te_counts)]) 
        }else{
          te_counts <- merge(te_counts, tmp$te_counts, by=c("Geneid", "Chr", "Start", "End", "Strand", "Length"))
        }
        # And we add the samplesheet from the region to our original samplesheet
        samplesheet <- rbind(samplesheet, tmp$samplesheet)
      }
    }
    # We return the count matrix with all pseudobulks (of all regions specified) and all samplesheets concatenated
    return(list("te_counts" = te_counts, "samplesheet" = samplesheet))
  }else{
    # If it's just one region, idk why you are calling this function, but here you go.
    region <- unlist(regions)
    return(read_te_counts_asap_region(region))
  }
}

3. Clustering Utility Functions

3.1 Cluster columns by group

Clusters pseudobulks (columns) based on a metadata category, e.g., celltype or region. Uses eigenvector decomposition of scaled expression for ordering and hierarchical clustering within groups.

# Cluster columns in heatmap based on a category (cell type, region, etc)
cluster_cols_by_group <- function(df, rows, group_cols, data_samplesheet, order = NA){
  # Calculate eigen values
    eigenvalues <- svd(t(scale(t(df))),nu=1,nv=1)$v
    scaledExpr <- scale(t(df[rows,]))
    averExpr <- rowMeans(scaledExpr, na.rm = TRUE)
    if(cor(averExpr,eigenvalues) < 0){
      eigenvalues <- -eigenvalues
    }
    index_eigen <- order(eigenvalues)
    # Add group variable in samplesheet
    # If more than one, we collapse those columns
    if(length(group_cols) > 1){
      data_samplesheet$Group <- apply(data_samplesheet[,group_cols,drop=F], 1, paste, collapse=' ')    
    }else{
      data_samplesheet$Group <- data_samplesheet[,group_cols]
    }
    index_reorder <- c()
    index_pre <- c(1:length(data_samplesheet$Group))
    # For each group
    for(eachgroup in unique(data_samplesheet$Group)){
      index_tempEigen <- index_eigen[index_eigen %in% index_pre[data_samplesheet$Group == eachgroup]]
      if(length(index_tempEigen) > 1){
        # we calculate the sample distance to each cluster of samples (in this case pseudobulks)
        sampleDist<-dist(t(df[,index_tempEigen]), method="euclidean")
        sampleClust <- hclust(sampleDist, method='complete')
        index_clust <- sampleClust$order
        if(cor(index_clust,c(1:length(index_tempEigen))) < 0){
          index_clust <- rev(index_clust)
        }  
      }else{
        index_clust <- 1
      }
      # Final order
      index_reorder <- c(index_reorder,index_tempEigen[index_clust])
    }
    return(index_reorder)
}

3.1 Cluster rows by group

Clusters TEs (rows) based on a group category (e.g., TE subfamily/type). Similar approach as column clustering but applied to rows.

# Cluster rows in heatmap based on a category (TE subfamily, etc)
cluster_rows_by_group <- function(df, group_rows, data_TE_annotation){
  # Calculate eigen values
    eigenvalues <- svd(t(scale(df)),nu=1,nv=1)$v
    scaledExpr <- scale(df)
    averExpr <- rowMeans(scaledExpr, na.rm = TRUE)
    if(cor(averExpr,eigenvalues) < 0){
      eigenvalues <- -eigenvalues
    }
    index_eigen <- order(eigenvalues)
    # Add group variable in samplesheet
    # If more than one, we collapse those columns
    
    if(length(group_rows) > 1){
      data_TE_annotation$Group <- apply(data_TE_annotation[,group_rows], 1, paste, collapse=' ')    
    }else{
      data_TE_annotation$Group <- data_TE_annotation[,group_rows]
    }
    index_reorder <- c()
    index_pre <- c(1:length(data_TE_annotation$Group))
    # For each group
    for(eachgroup in unique(data_TE_annotation$Group)){
      index_tempEigen <- index_eigen[index_eigen %in% index_pre[data_TE_annotation$Group == eachgroup]]
      # we calculate the sample distance to each cluster of samples (in this case pseudobulks)
      sampleDist<-dist(df[index_tempEigen,], method="euclidean")
      sampleClust<-hclust(sampleDist)
      index_clust <- sampleClust$order
      if(cor(index_clust,c(1:length(index_tempEigen))) < 0){
        index_clust <- rev(index_clust)
      }
      # Final order
      index_reorder <- c(index_reorder,index_tempEigen[index_clust])
    }
    return(index_reorder)
}

4. Main heatmap function

Purpose:

Generates normalized pseudobulk heatmaps for TEs or HERVs. ### Highlights: * Normalization by pseudobulk nuclei counts. * Log2 transformation and scaling. * Flexible clustering and ordering of columns and rows. * Annotation for both columns (metadata) and rows (TE types). * Optionally returns normalized data without plotting. ### Key Parameters: * region: brain region(s) to analyze. * tes: vector of TE IDs to include. * data: preloaded TE/HERV data to speed up repeated heatmaps. * group_cols: cluster columns within a group category. * group_rows: cluster rows within a group category. * index_reorder / index_row_reorder: specify custom column/row order. * filter_low_pseudocounts: remove pseudobulks with few nuclei.

Minimum arguments: brain region of interest (region) and TE ids as a vector (tes).

Note: given that it can be quite slow to load the matrices to create these heatmaps, and you might make several at the time, maybe you want to consider using the parameter data, which expects the output of read_te_counts_asap_multiregion().

asap_heatmap_snRNA <- function(region, 
                               tes, 
                               return_df = F, # Dont make a heatmap, just give me the data
                               show_rownames = F, # No ids (too large)
                               gaps_col = NULL, # Do you need gaps in the columns
                               gaps_row = NULL, # Do you need gaps in the rows
                               min_expression = 10,
                               scale = "none", # Not scaling by row by default
                               celltype = NA, # Plot a specific cell type?
                               data = NA, # Receive output of read_te_counts_asap_multiregion() to speed things up
                               title = "", 
                               group_cols = NA, # Cluster columns within a group category?
                               group_rows = NA, # Cluster rows within a group category?
                               prefix = NA, # Prefix for the reading of the matrix (TE or HERV)
                               exclude_clusters = NA, # Exclude a particular cluster?
                               index_reorder = NA, # Maybe you have already decided on the order of the columns? You can pass here their names as sample_clusters names from the samplesheets.
                               index_row_reorder = NA, # Same for rows
                               data_TE_annotation = NA,
                               annotation_cols = NA,
                               breaks = NA,
                               order_cols_groups = NA,
                               filter_low_pseudocounts = T
                               ){
  if(all(is.na(data))){ # If you havent given the data, read it
    data <- read_te_counts_asap_multiregion(region, prefix)    
  }
  if(!all(is.na(exclude_clusters))){ # If you want to exclude clusters, do that now
    data$samplesheet <- data$samplesheet[which(!data$samplesheet$cluster %in% as.character(exclude_clusters)),]
  }
  # We keep only the sample_clusters columns
  tokeep <- colnames(data$te_counts)[which(!colnames(data$te_counts) %in% c("Geneid", "Chr", "Start", "End", "Strand", "Length", "TE_subfamily", "TE_family", "TE_class"))]
  
  # Make sample_cluster variable in samplesheet
  data$samplesheet$sample_cluster <- paste(data$samplesheet$Sample, data$samplesheet$cluster, sep="_")
  # Keep only those that are present in the count matrix
  data$samplesheet <- data$samplesheet[which(data$samplesheet$sample_cluster %in% colnames(data$te_counts)),]
  # sample_cluster is now our pseudobulk ID
  rownames(data$samplesheet) <- data$samplesheet$sample_cluster
  
  if(length(nchar(region)) > 1){
    # For each of the regions, read the number of nuclei per cluster
    for(r in 1:length(region)){
      if(r == 1){
        # If it's the first iteration we can create that dataframe
        num_nuclei <- read.table(paste("/Volumes/MyPassport/ASAP/code/ASAP_PMDBS_snRNAseq/original/number_nuclei/",region[r],"_clusters.txt", sep=""), header = F, skip = 1)
      }else{
        # Otherwise, we can just concatenate to it
        num_nuclei <- rbind(num_nuclei, read.table(paste("/Volumes/MyPassport/ASAP/code/ASAP_PMDBS_snRNAseq/original/number_nuclei/",region[r],"_clusters.txt", sep=""), header = F, skip = 1))
      }
    }
  }else{
    # Same if it's just one region
    num_nuclei <- read.table(paste("/Volumes/MyPassport/ASAP/code/ASAP_PMDBS_snRNAseq/original/number_nuclei/",region, "_clusters.txt", sep=""), header = F, skip = 1)
  }
  
  colnames(num_nuclei) <- c("cluster", "num_nuclei")
  # There is a "total" row. I'll remove that for convenience
  num_nuclei <- num_nuclei[which(num_nuclei$cluster != "total"),]
  rownames(num_nuclei) <- num_nuclei$cluster
  
  if(filter_low_pseudocounts){
    # Just keep pseudobulks with at least 50 nuclei (arbitrary)
    num_nuclei <- num_nuclei[which(num_nuclei$num_nuclei > 50),] # Remove tiny pseudobulks
  }
  
  # From all samples_clusters
  samples_clusters <- colnames(data$te_counts[,data$samplesheet$sample_cluster])
  # Remove those that we dont have number of nuclei information from (tiny pseudobulks which we removed from the num_nuclei dataframe)
  samples_clusters <- samples_clusters[which(samples_clusters %in% num_nuclei$cluster)]
  
  # Make a copy of the count matrix with only those samples_clusters (pseudobulks)
  te_counts_norm_num <- data$te_counts[tes,samples_clusters]
  # We take note of the expressed elements, if an element is not expressed, this will result in NA and we will get an error later, so, let's remove that
  expressed_rows <- rownames(te_counts_norm_num)[which(rowSums(te_counts_norm_num) > min_expression)]
  te_counts_norm_num <- te_counts_norm_num[expressed_rows,]
  # Normalize counts by number of nuclei in cluster
  te_counts_norm_num[] <- mapply('/', te_counts_norm_num[,samples_clusters], num_nuclei[samples_clusters,"num_nuclei"])
  te_counts_norm_num$TE_id <- rownames(te_counts_norm_num)
  
  # Add cell type information to samplesheet
  data$samplesheet$celltype <- ifelse(data$samplesheet$cluster == "0", "0_ExcNeurons", 
                                      ifelse(data$samplesheet$cluster == "1", "1_InhNeurons", 
                                             ifelse(data$samplesheet$cluster == "2", "2_Astrocytes", 
                                                    ifelse(data$samplesheet$cluster == "3", "3_OPC", 
                                                           ifelse(data$samplesheet$cluster == "4", "4_Microglia", 
                                                                  ifelse(data$samplesheet$cluster == "5", "5_Oligodendrocytes", 
                                                                         ifelse(data$samplesheet$cluster == "6", "6_VLMC", 
                                                                                ifelse(data$samplesheet$cluster == "7", "7_Tcells", "Other?"))))))))
  
  # A simplified version of that
  data$samplesheet <- data$samplesheet %>% 
    mutate(celltype_simple = ifelse(celltype %in% c("0_ExcNeurons", "1_InhNeurons"), "Neurons", ifelse(celltype %in% c("2_Astrocytes","5_Oligodendrocytes", "3_OPC"), "Glia", "Microglia")))
  
  data$samplesheet <- data$samplesheet[order(data$samplesheet$celltype_simple, data$samplesheet$celltype, data$samplesheet$Region, data$samplesheet$Dx),]
  
  # If you want to just look at one cell type (cluster), we can just keep those 
  if(!is.na(celltype)){
    data$samplesheet <- data$samplesheet[which(data$samplesheet$cluster == celltype),] 
    te_counts_norm_num <- te_counts_norm_num[, which(colnames(te_counts_norm_num) %in% data$samplesheet$sample_cluster)]
  }
  
  # Let's clean the samplesheet to the columns we are going to be focusing on (no tiny pseudobulks, no clusters we are not interested in)
  data$samplesheet <- data$samplesheet[which(data$samplesheet$sample_cluster %in% colnames(te_counts_norm_num)),]
  # Scale (x1000) and log2 with a 1 as pseudocount
  data_heatmap <- log2(te_counts_norm_num[which(rownames(te_counts_norm_num) %in% tes),data$samplesheet$sample_cluster]*1000+1) # Here i just changed te_counts_norm_num$TE_id for rownames(te_counts_norm_num)
  
  # If we want to cluster columns by a particular group/category, here is where that happens
  # If we dont, we simply set cluster_cols as TRUE
  if(all(is.na(group_cols))){
    cluster_cols = TRUE
  }else{
    # If we have a defined order we want to have, cool, we go to the else of this condition, 
    # Otherwise, we need to cluster groups
    if(all(is.na(index_reorder))){
      # Set cluster_cols as FALSE
      cluster_cols = FALSE
      index_reorder <- cluster_cols_by_group(df = data_heatmap, rows= expressed_rows, group_cols = group_cols, data_samplesheet = data$samplesheet, order = order_cols_groups)
      data$samplesheet$index_orig <- 1:nrow(data$samplesheet)
      tmp <- data$samplesheet[index_reorder,]
      tmp_split <- split(tmp, f = tmp[,group_cols])
      tmp <- do.call(rbind, tmp_split[order_cols_groups])
      index_reorder <- tmp$index_orig
    }
    # Save that order to return 
    index_sample_clusters <- data$samplesheet[index_reorder,"sample_cluster"]
    data$samplesheet <- data$samplesheet[index_reorder,]
  }
  
  # Order data for heatmap
  data_heatmap <- data_heatmap[,data$samplesheet$sample_cluster]
  # Merge with num_nuclei to add that annotation at the top of the heatmap
  data$samplesheet <- merge(data$samplesheet, num_nuclei, by.x="sample_cluster", by.y="cluster")
  rownames(data$samplesheet) <- data$samplesheet$sample_cluster
  
  if(all(is.na(group_rows))){
    cluster_rows = FALSE
  }else{
    cluster_rows = FALSE
    if(all(is.na(index_row_reorder))){
      data_TE_annotation <- data_TE_annotation[which(data_TE_annotation$TE_id %in% rownames(data_heatmap)),]
      index_TE_id <- cluster_rows_by_group(df = data_heatmap, group_rows = "type", data_TE_annotation = data_TE_annotation)
      # If we are clustering per group, let's order data for heatmap and the annotation for TEs
      data_TE_annotation <- data_TE_annotation[index_TE_id,]
      data_heatmap <- data_heatmap[as.character(data_TE_annotation$TE_id),]
      index_row_reorder <- rownames(data_heatmap)
      gaps_row <- which(!duplicated(data_TE_annotation$type))[-1]-1 # Add a gap between groups
    }else{
      data_heatmap <- data_heatmap[index_row_reorder,]
      cluster_rows = FALSE
    }
  }
  
  # If you dont want a heatmap, here goes the data
  if(return_df){
    return(list("norm_counts" = te_counts_norm_num,
                "samplesheet" = data$samplesheet))
  }else{
    # If you do want a heatmap, here it comes (and the order of the columns, in case you need it for later)
    getPalette = colorRampPalette(brewer.pal(11, "RdYlBu"))
    col.pal <- rev(getPalette(60))[8:60]
    return(list("heatmap" = pheatmap(data_heatmap, 
                    show_rownames = show_rownames,
                    annotation_col = data$samplesheet[,c("celltype", "celltype_simple", "Dx", "Region")],
                    show_colnames = F, 
                    cluster_rows = cluster_rows,
                    cluster_cols = cluster_cols,
                    gaps_col = gaps_col,
                    gaps_row = gaps_row,
                    border_color = NA, 
                    breaks = breaks,
                    color = col.pal,
                    scale = scale,
                    annotation_row = data_TE_annotation[,"type", drop=F],
                    annotation_colors = annotation_cols,
                    main = title),
           "order_cols" = index_sample_clusters,
           "order_rows" = index_row_reorder))  
  }
}

5. Column annotation colors

Defines colors for: * Brain region * Simplified cell type (celltype_simple) * Cell type * Diagnosis (PD vs. control) * TE type (L1 vs. HERV)

These are used in heatmap column and row annotations.

annotation_cols <- list("Region" = c("SN" = "#46c8e8",
                                                          "PUT" = "#ed9924",
                                                          "PFC" = "#db84da",
                                                          "AMY" = "#7ac47c"),
                                             "celltype_simple" = c("Neurons" = "#a0dbb0",
                                                                   "Glia" = "#a1a8e6",
                                                                   "Microglia" = "#e0e0e0"),
                                             "celltype" = c("0_ExcNeurons" = "#80e8d8",
                                                            "1_InhNeurons" = "#f5be51",
                                                            "2_Astrocytes" = "#c69deb",
                                                            "3_OPC" = "#f55d42",
                                                            "4_Microglia" = "#688db3",
                                                            "5_Oligodendrocytes" = "#ed8337",
                                                            "6_VLMC" = "#7bbd75",
                                                            "7_Tcells" = "#eb7878"),
                                             "Dx" = c("PD" = "#8fd9ca",
                                                      "Ctl" = "lightgrey"),
                                             "type" = c("only" = "#a0dbb0",
                                                        "put" = "#388db3"))

6. Read expressed TE IDs

Load TEs that were detected as expressed in deep bulk RNAseq for each brain region.

# L1s
L1s_sorted_pfc <- read.table("/Volumes/MyPassport/ASAP/code/ASAP_PMDBS_bulkRNAseq/results/tables/expressed_FL_L1HS_L1PA3_expressed_sorted_mean_expression_PFC.tab")$V1
L1s_sorted_put <- read.table("/Volumes/MyPassport/ASAP/code/ASAP_PMDBS_bulkRNAseq/results/tables/expressed_FL_L1HS_L1PA3_expressed_sorted_mean_expression_PUT.tab")$V1
L1s_sorted_sn <- read.table("/Volumes/MyPassport/ASAP/code/ASAP_PMDBS_bulkRNAseq/results/tables/expressed_FL_L1HS_L1PA3_expressed_sorted_mean_expression_SN.tab")$V1
L1s_sorted_amy <- read.table("/Volumes/MyPassport/ASAP/code/ASAP_PMDBS_bulkRNAseq/results/tables/expressed_FL_L1HS_L1PA3_expressed_sorted_mean_expression_AMY.tab")$V1

# HERVs
HERVs_sorted_pfc <- read.table("/Volumes/MyPassport/ASAP/code/ASAP_PMDBS_bulkRNAseq/results/tables/expressed_fl_hervs_expressed_sorted_mean_expression_PFC.tab")$V1
HERVs_sorted_put <- read.table("/Volumes/MyPassport/ASAP/code/ASAP_PMDBS_bulkRNAseq/results/tables/expressed_fl_hervs_expressed_sorted_mean_expression_PUT.tab")$V1
HERVs_sorted_sn <- read.table("/Volumes/MyPassport/ASAP/code/ASAP_PMDBS_bulkRNAseq/results/tables/expressed_fl_hervs_expressed_sorted_mean_expression_SN.tab")$V1
HERVs_sorted_amy <- read.table("/Volumes/MyPassport/ASAP/code/ASAP_PMDBS_bulkRNAseq/results/tables/expressed_fl_hervs_expressed_sorted_mean_expression_AMY.tab")$V1

7. Read count matrices

Load and merge TE (repeatmasker counts) and HERV (retrotector counts) pseudobulk matrices across brain regions for heatmaps.

# Read count matrices
TE_data <- read_te_counts_asap_multiregion(regions = c("SN", "PUT", "PFC", "AMY"), prefix = "TE")

## [1] "More than one region"
## [1] "Region SN"
## [1] "0"
## [1] "SN"
## [1] "1"
## [1] "SN"
## [1] "2"
## [1] "SN"
## [1] "3"
## [1] "SN"
## [1] "4"
## [1] "SN"
## [1] "5"
## [1] "SN"
## [1] "6"
## [1] "SN"
## [1] "7"
## [1] "SN"
## [1] "Region PUT"
## [1] "0"
## [1] "PUT"
## [1] "1"
## [1] "PUT"
## [1] "2"
## [1] "PUT"
## [1] "3"
## [1] "PUT"
## [1] "4"
## [1] "PUT"
## [1] "5"
## [1] "PUT"
## [1] "6"
## [1] "PUT"
## [1] "7"
## [1] "PUT"
## [1] "Region PFC"
## [1] "0"
## [1] "PFC"
## [1] "1"
## [1] "PFC"
## [1] "2"
## [1] "PFC"
## [1] "3"
## [1] "PFC"
## [1] "4"
## [1] "PFC"
## [1] "5"
## [1] "PFC"
## [1] "6"
## [1] "PFC"
## [1] "7"
## [1] "PFC"
## [1] "Region AMY"
## [1] "0"
## [1] "AMY"
## [1] "1"
## [1] "AMY"
## [1] "2"
## [1] "AMY"
## [1] "3"
## [1] "AMY"
## [1] "4"
## [1] "AMY"
## [1] "5"
## [1] "AMY"
## [1] "6"
## [1] "AMY"
## [1] "7"
## [1] "AMY"

HERV_data <- read_te_counts_asap_multiregion(regions = c("SN", "PUT", "PFC", "AMY"), prefix = "HERV")

## [1] "More than one region"
## [1] "Region SN"
## [1] "0"
## [1] "SN"
## [1] "1"
## [1] "SN"
## [1] "2"
## [1] "SN"
## [1] "3"
## [1] "SN"
## [1] "4"
## [1] "SN"
## [1] "5"
## [1] "SN"
## [1] "6"
## [1] "SN"
## [1] "7"
## [1] "SN"
## [1] "Region PUT"
## [1] "0"
## [1] "PUT"
## [1] "1"
## [1] "PUT"
## [1] "2"
## [1] "PUT"
## [1] "3"
## [1] "PUT"
## [1] "4"
## [1] "PUT"
## [1] "5"
## [1] "PUT"
## [1] "6"
## [1] "PUT"
## [1] "7"
## [1] "PUT"
## [1] "Region PFC"
## [1] "0"
## [1] "PFC"
## [1] "1"
## [1] "PFC"
## [1] "2"
## [1] "PFC"
## [1] "3"
## [1] "PFC"
## [1] "4"
## [1] "PFC"
## [1] "5"
## [1] "PFC"
## [1] "6"
## [1] "PFC"
## [1] "7"
## [1] "PFC"
## [1] "Region AMY"
## [1] "0"
## [1] "AMY"
## [1] "1"
## [1] "AMY"
## [1] "2"
## [1] "AMY"
## [1] "3"
## [1] "AMY"
## [1] "4"
## [1] "AMY"
## [1] "5"
## [1] "AMY"
## [1] "6"
## [1] "AMY"
## [1] "7"
## [1] "AMY"

# Row binding of HERVs to the repeatmasker count matrix
TE_data$te_counts <- rbind(TE_data$te_counts[,colnames(TE_data$te_counts)], HERV_data$te_counts[,colnames(TE_data$te_counts)])

8. Generate heatmaps

8.1 Combine TE IDs across regions

Prepare TE IDs and row annotations for plotting heatmaps across all regions

# All together to share scale
tes <- unique(c(HERVs_sorted_pfc, HERVs_sorted_put, HERVs_sorted_sn, HERVs_sorted_amy, L1s_sorted_pfc, L1s_sorted_put, L1s_sorted_sn, L1s_sorted_amy))
data_TE_annotation <- data.frame("TE_id" = tes,
                                 "type" = ifelse(startsWith(tes, "HERV"), "HERV", "L1"))
rownames(data_TE_annotation) <- data_TE_annotation$TE_id
order_cols_celltype <- c("0_ExcNeurons", "1_InhNeurons", "2_Astrocytes", "3_OPC", "5_Oligodendrocytes", "4_Microglia", "6_VLMC", "7_Tcells")
# Save the heatmap to extract the row order
annotation_cols$type <- NULL

8.2 Pseudobulk heatmaps sorted by expression levels

• Heatmap visualization of expressed >6kbp L1HS-L1PA3 and HERVs on pseudobulks with more than 50 nuclei (line 318).
• index_row_reorder is set to the ranked TE list based on expression values in the specific brain region (max to min expression).
• Excluded clusters 6 (VLMC) and 7 (Tcells) due to low number of nuclei.

asap_heatmap_snRNA(region = c("PFC"), 
                   tes = data_TE_annotation[which(data_TE_annotation$type == "L1"),"TE_id"], 
                   return_df = F, 
                   breaks = seq(0,15,length.out = 52), 
                   data = TE_data, 
                   group_cols = c("celltype"), 
                   index_row_reorder = c(L1s_sorted_pfc),
                   order_cols_groups = order_cols_celltype,
                   title = "PFC L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
                   annotation_cols = annotation_cols)

## $heatmap
## 
## $order_cols
##   [1] "AA_ASAP90_ctrl_NP16-293_PFC_0"    "AA_ASAP89_ctrl_NP16-284_PFC_0"   
##   [3] "AA_ASAP152_PD_NP19-91_PFC_0"      "AA_ASAP116_PD_NP22-55_PFC_0"     
##   [5] "ASAP155_ctrl_NP23-21_PFC_0"       "AA_ASAP151_PD_NP17-232_PFC_0"    
##   [7] "DA795_ASAP55_ctrl_NP19-37_PFC_0"  "DA480_ASAP15_ctrl_NP16-21_PFC_0" 
##   [9] "DA430_ASAP9_PD_NP16-162_PFC_0"    "DA490_ASAP11_PD_P73_PFC_0"       
##  [11] "AA_ASAP83_NP16-119_ctrl_PFC_0"    "DA810_ASAP34_PD_NP18-304_PFC_0"  
##  [13] "DA428_ASAP13_ctrl_NP16-161_PFC_0" "DA488_ASAP16_ctrl_PT231_PFC_0"   
##  [15] "DA806_ASAP58_ctrl_NP19-45_PFC_0"  "DA432_ASAP12_PD_P74_PFC_0"       
##  [17] "DA509_ASAP36_PD_NP19-16_PFC_0"    "AA_ASAP86_NP18-148_ctrl_PFC_0"   
##  [19] "AA_ASAP80_PD_NP21-57_PFC_0"       "DA476_ASAP10_PD_NP16-25_PFC_0"   
##  [21] "AA_ASAP85_NP18-46_ctrl_PFC_0"     "AA_ASAP91_ctrl_NP17-20_PFC_0"    
##  [23] "MJ_ASAP14_ctrl_NP16-164_PFC_0"    "AA_ASAP145_ctrl_NP19-218_PFC_0"  
##  [25] "AA_ASAP81_PD_NP21-208_PFC_0"      "DA777_ASAP28_PD_NP17-191_PFC_0"  
##  [27] "DA499_ASAP44_PD_NP19-255_PFC_0"   "DA809_ASAP30_PD_NP18-117_PFC_0"  
##  [29] "AA_ASAP82_PD_NP21-217_PFC_0"      "AA_ASAP153_ctrl_NP19-137_PFC_0"  
##  [31] "DA804_ASAP49_ctrl_NP18-159_PFC_0" "DA775_ASAP22_PD_NP16-269_PFC_0"  
##  [33] "DA813_ASAP17_PD_NP16-140_PFC_0"   "DA775_ASAP22_PD_NP16-269_PFC_1"  
##  [35] "DA809_ASAP30_PD_NP18-117_PFC_1"   "DA804_ASAP49_ctrl_NP18-159_PFC_1"
##  [37] "AA_ASAP85_NP18-46_ctrl_PFC_1"     "AA_ASAP116_PD_NP22-55_PFC_1"     
##  [39] "MJ_ASAP14_ctrl_NP16-164_PFC_1"    "AA_ASAP91_ctrl_NP17-20_PFC_1"    
##  [41] "ASAP155_ctrl_NP23-21_PFC_1"       "DA509_ASAP36_PD_NP19-16_PFC_1"   
##  [43] "DA490_ASAP11_PD_P73_PFC_1"        "AA_ASAP90_ctrl_NP16-293_PFC_1"   
##  [45] "AA_ASAP89_ctrl_NP16-284_PFC_1"    "AA_ASAP152_PD_NP19-91_PFC_1"     
##  [47] "DA480_ASAP15_ctrl_NP16-21_PFC_1"  "AA_ASAP145_ctrl_NP19-218_PFC_1"  
##  [49] "AA_ASAP151_PD_NP17-232_PFC_1"     "AA_ASAP86_NP18-148_ctrl_PFC_1"   
##  [51] "DA476_ASAP10_PD_NP16-25_PFC_1"    "DA430_ASAP9_PD_NP16-162_PFC_1"   
##  [53] "AA_ASAP83_NP16-119_ctrl_PFC_1"    "AA_ASAP81_PD_NP21-208_PFC_1"     
##  [55] "AA_ASAP82_PD_NP21-217_PFC_1"      "DA777_ASAP28_PD_NP17-191_PFC_1"  
##  [57] "AA_ASAP80_PD_NP21-57_PFC_1"       "DA810_ASAP34_PD_NP18-304_PFC_1"  
##  [59] "DA806_ASAP58_ctrl_NP19-45_PFC_1"  "DA499_ASAP44_PD_NP19-255_PFC_1"  
##  [61] "DA432_ASAP12_PD_P74_PFC_1"        "DA488_ASAP16_ctrl_PT231_PFC_1"   
##  [63] "DA428_ASAP13_ctrl_NP16-161_PFC_1" "AA_ASAP153_ctrl_NP19-137_PFC_1"  
##  [65] "DA795_ASAP55_ctrl_NP19-37_PFC_1"  "DA808_ASAP41_PD_NP19-108_PFC_2"  
##  [67] "DA775_ASAP22_PD_NP16-269_PFC_2"   "DA809_ASAP30_PD_NP18-117_PFC_2"  
##  [69] "DA804_ASAP49_ctrl_NP18-159_PFC_2" "DA785_ASAP47_ctrl_NP17-256_PFC_2"
##  [71] "AA_ASAP84_NP17-216_ctrl_PFC_2"    "AA_ASAP154_ctrl_NP21-04_PFC_2"   
##  [73] "AA_ASAP91_ctrl_NP17-20_PFC_2"     "AA_ASAP150_PD_NP16-285_PFC_2"    
##  [75] "MJ_ASAP14_ctrl_NP16-164_PFC_2"    "DA480_ASAP15_ctrl_NP16-21_PFC_2" 
##  [77] "DA499_ASAP44_PD_NP19-255_PFC_2"   "AA_ASAP152_PD_NP19-91_PFC_2"     
##  [79] "DA428_ASAP13_ctrl_NP16-161_PFC_2" "AA_ASAP153_ctrl_NP19-137_PFC_2"  
##  [81] "DA490_ASAP11_PD_P73_PFC_2"        "AA_ASAP81_PD_NP21-208_PFC_2"     
##  [83] "DA432_ASAP12_PD_P74_PFC_2"        "ASAP155_ctrl_NP23-21_PFC_2"      
##  [85] "DA509_ASAP36_PD_NP19-16_PFC_2"    "AA_ASAP90_ctrl_NP16-293_PFC_2"   
##  [87] "AA_ASAP145_ctrl_NP19-218_PFC_2"   "DA476_ASAP10_PD_NP16-25_PFC_2"   
##  [89] "AA_ASAP80_PD_NP21-57_PFC_2"       "DA806_ASAP58_ctrl_NP19-45_PFC_2" 
##  [91] "DA810_ASAP34_PD_NP18-304_PFC_2"   "AA_ASAP89_ctrl_NP16-284_PFC_2"   
##  [93] "DA430_ASAP9_PD_NP16-162_PFC_2"    "AA_ASAP151_PD_NP17-232_PFC_2"    
##  [95] "AA_ASAP83_NP16-119_ctrl_PFC_2"    "DA488_ASAP16_ctrl_PT231_PFC_2"   
##  [97] "AA_ASAP82_PD_NP21-217_PFC_2"      "DA795_ASAP55_ctrl_NP19-37_PFC_2" 
##  [99] "AA_ASAP86_NP18-148_ctrl_PFC_2"    "AA_ASAP116_PD_NP22-55_PFC_2"     
## [101] "AA_ASAP84_NP17-216_ctrl_PFC_3"    "AA_ASAP116_PD_NP22-55_PFC_3"     
## [103] "AA_ASAP86_NP18-148_ctrl_PFC_3"    "AA_ASAP145_ctrl_NP19-218_PFC_3"  
## [105] "AA_ASAP151_PD_NP17-232_PFC_3"     "DA777_ASAP28_PD_NP17-191_PFC_3"  
## [107] "DA430_ASAP9_PD_NP16-162_PFC_3"    "AA_ASAP83_NP16-119_ctrl_PFC_3"   
## [109] "DA499_ASAP44_PD_NP19-255_PFC_3"   "DA810_ASAP34_PD_NP18-304_PFC_3"  
## [111] "AA_ASAP80_PD_NP21-57_PFC_3"       "AA_ASAP82_PD_NP21-217_PFC_3"     
## [113] "DA806_ASAP58_ctrl_NP19-45_PFC_3"  "AA_ASAP150_PD_NP16-285_PFC_3"    
## [115] "DA432_ASAP12_PD_P74_PFC_3"        "AA_ASAP154_ctrl_NP21-04_PFC_3"   
## [117] "AA_ASAP91_ctrl_NP17-20_PFC_3"     "ASAP155_ctrl_NP23-21_PFC_3"      
## [119] "AA_ASAP89_ctrl_NP16-284_PFC_3"    "AA_ASAP152_PD_NP19-91_PFC_3"     
## [121] "DA490_ASAP11_PD_P73_PFC_3"        "DA480_ASAP15_ctrl_NP16-21_PFC_3" 
## [123] "DA509_ASAP36_PD_NP19-16_PFC_3"    "AA_ASAP90_ctrl_NP16-293_PFC_3"   
## [125] "DA488_ASAP16_ctrl_PT231_PFC_3"    "DA428_ASAP13_ctrl_NP16-161_PFC_3"
## [127] "DA775_ASAP22_PD_NP16-269_PFC_3"   "DA785_ASAP47_ctrl_NP17-256_PFC_3"
## [129] "MJ_ASAP14_ctrl_NP16-164_PFC_3"    "DA795_ASAP55_ctrl_NP19-37_PFC_3" 
## [131] "DA476_ASAP10_PD_NP16-25_PFC_3"    "DA804_ASAP49_ctrl_NP18-159_PFC_3"
## [133] "DA809_ASAP30_PD_NP18-117_PFC_3"   "AA_ASAP154_ctrl_NP21-04_PFC_5"   
## [135] "AA_ASAP84_NP17-216_ctrl_PFC_5"    "DA799_ASAP19_PD_NP16-160_PFC_5"  
## [137] "DA806_ASAP58_ctrl_NP19-45_PFC_5"  "DA430_ASAP9_PD_NP16-162_PFC_5"   
## [139] "AA_ASAP90_ctrl_NP16-293_PFC_5"    "AA_ASAP83_NP16-119_ctrl_PFC_5"   
## [141] "DA428_ASAP13_ctrl_NP16-161_PFC_5" "AA_ASAP85_NP18-46_ctrl_PFC_5"    
## [143] "DA480_ASAP15_ctrl_NP16-21_PFC_5"  "AA_ASAP152_PD_NP19-91_PFC_5"     
## [145] "DA499_ASAP44_PD_NP19-255_PFC_5"   "AA_ASAP80_PD_NP21-57_PFC_5"      
## [147] "AA_ASAP82_PD_NP21-217_PFC_5"      "DA488_ASAP16_ctrl_PT231_PFC_5"   
## [149] "DA810_ASAP34_PD_NP18-304_PFC_5"   "AA_ASAP86_NP18-148_ctrl_PFC_5"   
## [151] "AA_ASAP145_ctrl_NP19-218_PFC_5"   "MJ_ASAP14_ctrl_NP16-164_PFC_5"   
## [153] "DA432_ASAP12_PD_P74_PFC_5"        "DA490_ASAP11_PD_P73_PFC_5"       
## [155] "DA509_ASAP36_PD_NP19-16_PFC_5"    "AA_ASAP89_ctrl_NP16-284_PFC_5"   
## [157] "AA_ASAP91_ctrl_NP17-20_PFC_5"     "AA_ASAP153_ctrl_NP19-137_PFC_5"  
## [159] "ASAP155_ctrl_NP23-21_PFC_5"       "DA813_ASAP17_PD_NP16-140_PFC_5"  
## [161] "DA785_ASAP47_ctrl_NP17-256_PFC_5" "DA808_ASAP41_PD_NP19-108_PFC_5"  
## [163] "AA_ASAP116_PD_NP22-55_PFC_5"      "AA_ASAP150_PD_NP16-285_PFC_5"    
## [165] "DA777_ASAP28_PD_NP17-191_PFC_5"   "AA_ASAP151_PD_NP17-232_PFC_5"    
## [167] "DA476_ASAP10_PD_NP16-25_PFC_5"    "DA795_ASAP55_ctrl_NP19-37_PFC_5" 
## [169] "DA804_ASAP49_ctrl_NP18-159_PFC_5" "DA809_ASAP30_PD_NP18-117_PFC_5"  
## [171] "DA775_ASAP22_PD_NP16-269_PFC_5"   "AA_ASAP147_ctrl_NP22-37_PFC_5"   
## [173] "ASAP155_ctrl_NP23-21_PFC_4"       "AA_ASAP90_ctrl_NP16-293_PFC_4"   
## [175] "MJ_ASAP14_ctrl_NP16-164_PFC_4"    "DA499_ASAP44_PD_NP19-255_PFC_4"  
## [177] "DA490_ASAP11_PD_P73_PFC_4"        "DA480_ASAP15_ctrl_NP16-21_PFC_4" 
## [179] "DA432_ASAP12_PD_P74_PFC_4"        "AA_ASAP145_ctrl_NP19-218_PFC_4"  
## [181] "AA_ASAP89_ctrl_NP16-284_PFC_4"    "DA428_ASAP13_ctrl_NP16-161_PFC_4"
## [183] "AA_ASAP151_PD_NP17-232_PFC_4"     "DA808_ASAP41_PD_NP19-108_PFC_4"  
## [185] "DA795_ASAP55_ctrl_NP19-37_PFC_4"  "DA775_ASAP22_PD_NP16-269_PFC_4"  
## [187] "DA476_ASAP10_PD_NP16-25_PFC_4"    "AA_ASAP86_NP18-148_ctrl_PFC_4"   
## [189] "AA_ASAP83_NP16-119_ctrl_PFC_4"    "DA804_ASAP49_ctrl_NP18-159_PFC_4"
## [191] "DA806_ASAP58_ctrl_NP19-45_PFC_4"  "AA_ASAP152_PD_NP19-91_PFC_4"     
## [193] "AA_ASAP80_PD_NP21-57_PFC_4"       "AA_ASAP82_PD_NP21-217_PFC_4"     
## [195] "DA488_ASAP16_ctrl_PT231_PFC_4"    "DA430_ASAP9_PD_NP16-162_PFC_4"   
## [197] "AA_ASAP116_PD_NP22-55_PFC_4"      "DA428_ASAP13_ctrl_NP16-161_PFC_6"
## [199] "AA_ASAP89_ctrl_NP16-284_PFC_6"    "AA_ASAP152_PD_NP19-91_PFC_6"     
## [201] "MJ_ASAP14_ctrl_NP16-164_PFC_6"    "DA785_ASAP47_ctrl_NP17-256_PFC_6"
## 
## $order_rows
##   [1] "L1PA2_dup1230"  "L1PA2_dup848"   "L1PA2_dup791"   "L1HS_dup1462"  
##   [5] "L1PA2_dup4403"  "L1PA3_dup398"   "L1PA2_dup585"   "L1PA2_dup513"  
##   [9] "L1PA3_dup10686" "L1HS_dup337"    "L1PA3_dup1010"  "L1PA3_dup4994" 
##  [13] "L1PA3_dup8173"  "L1PA2_dup663"   "L1PA2_dup234"   "L1HS_dup124"   
##  [17] "L1PA3_dup2557"  "L1HS_dup455"    "L1PA3_dup8903"  "L1PA3_dup10285"
##  [21] "L1PA3_dup2204"  "L1PA2_dup4651"  "L1PA2_dup2245"  "L1PA2_dup922"  
##  [25] "L1PA2_dup378"   "L1PA3_dup7864"  "L1PA3_dup761"   "L1PA3_dup10119"
##  [29] "L1PA2_dup1621"  "L1PA3_dup2413"  "L1PA3_dup4492"  "L1PA3_dup2744" 
##  [33] "L1PA2_dup3736"  "L1PA2_dup4074"  "L1PA3_dup10297" "L1PA2_dup37"   
##  [37] "L1PA2_dup1462"  "L1HS_dup1324"   "L1PA3_dup400"   "L1PA3_dup4888" 
##  [41] "L1PA3_dup8663"  "L1PA2_dup949"   "L1PA3_dup527"   "L1PA3_dup1651" 
##  [45] "L1PA3_dup9021"  "L1PA2_dup39"    "L1PA2_dup4838"  "L1PA3_dup3102" 
##  [49] "L1PA3_dup1710"  "L1PA3_dup5928"  "L1PA3_dup9430"  "L1PA2_dup4612" 
##  [53] "L1PA3_dup8872"  "L1PA2_dup1298"  "L1PA3_dup8522"  "L1PA3_dup2517" 
##  [57] "L1PA3_dup1"     "L1PA2_dup559"   "L1PA3_dup4668"  "L1PA3_dup2919" 
##  [61] "L1PA3_dup872"   "L1PA3_dup4118"  "L1PA3_dup748"   "L1PA2_dup2504" 
##  [65] "L1PA3_dup10072" "L1PA3_dup5337"  "L1PA3_dup6385"  "L1PA2_dup927"  
##  [69] "L1PA3_dup4393"  "L1HS_dup444"    "L1PA3_dup1756"  "L1HS_dup916"   
##  [73] "L1PA3_dup4891"  "L1PA3_dup4709"  "L1PA3_dup6929"  "L1HS_dup514"   
##  [77] "L1PA2_dup2720"  "L1PA2_dup2047"  "L1PA2_dup1379"  "L1PA2_dup2408" 
##  [81] "L1PA2_dup4620"  "L1PA3_dup9946"  "L1HS_dup788"    "L1PA2_dup109"  
##  [85] "L1PA3_dup8007"  "L1PA3_dup1428"  "L1PA3_dup9280"  "L1PA3_dup2593" 
##  [89] "L1PA2_dup4430"  "L1PA2_dup2091"  "L1PA2_dup526"   "L1PA3_dup529"  
##  [93] "L1PA2_dup3484"  "L1PA2_dup2289"  "L1PA3_dup3168"  "L1PA2_dup4936" 
##  [97] "L1HS_dup1014"   "L1PA3_dup1311"  "L1HS_dup1330"   "L1PA3_dup8420" 
## [101] "L1PA3_dup373"   "L1PA3_dup8506"  "L1PA2_dup410"   "L1PA3_dup2760" 
## [105] "L1PA2_dup2343"  "L1PA3_dup10740" "L1PA2_dup3425"  "L1HS_dup1182"  
## [109] "L1PA2_dup4053"  "L1PA2_dup1953"  "L1PA3_dup2551"  "L1PA2_dup2791" 
## [113] "L1PA3_dup1723"  "L1PA2_dup4901"  "L1PA2_dup1398"  "L1PA2_dup737"  
## [117] "L1PA2_dup2680"  "L1PA3_dup7470"  "L1PA2_dup3292"  "L1PA2_dup423"  
## [121] "L1PA3_dup7605"  "L1PA2_dup142"   "L1HS_dup35"     "L1PA3_dup10525"
## [125] "L1HS_dup138"    "L1PA3_dup4277"  "L1PA3_dup3954"  "L1PA2_dup3771" 
## [129] "L1PA2_dup3607"  "L1PA3_dup1988"  "L1PA3_dup5514"  "L1PA3_dup6008" 
## [133] "L1PA3_dup6147"  "L1PA2_dup2385"  "L1HS_dup1357"   "L1PA3_dup6002" 
## [137] "L1PA2_dup662"   "L1PA2_dup3136"  "L1PA3_dup3758"  "L1PA2_dup4775" 
## [141] "L1PA2_dup3589"  "L1PA3_dup6457"  "L1PA3_dup4804"  "L1PA3_dup5680" 
## [145] "L1PA3_dup3484"  "L1PA3_dup1547"  "L1PA3_dup2393"  "L1PA2_dup1476" 
## [149] "L1HS_dup240"    "L1PA2_dup130"   "L1PA2_dup2969"  "L1PA3_dup3586" 
## [153] "L1HS_dup429"    "L1PA3_dup6317"  "L1HS_dup449"    "L1PA2_dup3773" 
## [157] "L1HS_dup62"     "L1HS_dup649"    "L1PA3_dup3323"  "L1PA3_dup2272" 
## [161] "L1PA3_dup2721"  "L1PA2_dup4335"  "L1HS_dup370"    "L1PA2_dup1490" 
## [165] "L1HS_dup1339"   "L1PA2_dup200"   "L1PA3_dup9734"  "L1PA2_dup2180" 
## [169] "L1PA3_dup358"   "L1PA3_dup7821"  "L1PA3_dup6036"  "L1PA2_dup3531" 
## [173] "L1PA3_dup5121"  "L1PA2_dup2863"  "L1PA2_dup2164"  "L1PA2_dup1760" 
## [177] "L1PA3_dup5866"  "L1HS_dup995"    "L1PA3_dup5106"  "L1PA3_dup561"  
## [181] "L1HS_dup163"    "L1HS_dup379"    "L1PA2_dup2909"  "L1PA3_dup1550" 
## [185] "L1PA3_dup2389"  "L1HS_dup111"    "L1PA2_dup4548"  "L1PA2_dup3805" 
## [189] "L1PA3_dup7862"  "L1PA2_dup678"   "L1PA3_dup4487"  "L1PA2_dup1770" 
## [193] "L1PA3_dup9373"  "L1PA3_dup8520"  "L1PA2_dup741"   "L1PA2_dup1653" 
## [197] "L1PA3_dup9256"  "L1PA3_dup4885"  "L1PA2_dup4030"  "L1PA3_dup1528" 
## [201] "L1PA3_dup2357"  "L1PA2_dup16"    "L1HS_dup1536"   "L1PA3_dup9473" 
## [205] "L1PA3_dup1937"  "L1PA3_dup7947"  "L1PA3_dup128"   "L1PA2_dup3742" 
## [209] "L1PA2_dup4421"  "L1HS_dup879"    "L1PA2_dup1560"  "L1PA2_dup4262" 
## [213] "L1HS_dup1104"   "L1PA3_dup6434"  "L1PA2_dup675"   "L1PA3_dup3863" 
## [217] "L1PA3_dup8525"  "L1HS_dup948"    "L1PA3_dup9095"  "L1PA3_dup5745" 
## [221] "L1PA3_dup10011" "L1PA2_dup2506"  "L1PA3_dup1114"  "L1PA3_dup3763" 
## [225] "L1PA3_dup1770"  "L1PA2_dup1778"  "L1PA2_dup935"   "L1PA3_dup1800" 
## [229] "L1PA3_dup4603"  "L1PA3_dup8891"  "L1PA2_dup4226"  "L1PA3_dup3306" 
## [233] "L1PA3_dup1554"  "L1PA3_dup3404"  "L1PA3_dup6692"  "L1PA2_dup3664" 
## [237] "L1PA3_dup2662"  "L1PA3_dup5534"  "L1HS_dup244"    "L1HS_dup632"   
## [241] "L1PA3_dup5207"  "L1PA2_dup4440"  "L1PA3_dup8571"  "L1PA3_dup4884" 
## [245] "L1HS_dup1478"   "L1PA2_dup4596"  "L1PA3_dup6436"  "L1PA3_dup3941" 
## [249] "L1HS_dup191"    "L1PA3_dup9702"  "L1PA3_dup7951"  "L1PA2_dup1752" 
## [253] "L1PA3_dup1264"  "L1PA2_dup1933"  "L1PA3_dup3968"  "L1HS_dup1286"  
## [257] "L1HS_dup579"    "L1PA3_dup978"   "L1PA3_dup6550"  "L1PA2_dup3437" 
## [261] "L1PA2_dup2860"  "L1PA3_dup7637"  "L1PA2_dup1112"  "L1PA3_dup5047" 
## [265] "L1PA2_dup221"   "L1HS_dup270"    "L1PA2_dup1331"  "L1HS_dup405"   
## [269] "L1PA2_dup4043"  "L1PA2_dup2155"  "L1PA2_dup1749"  "L1PA3_dup345"  
## [273] "L1PA3_dup3757"  "L1PA3_dup4349"  "L1PA2_dup360"   "L1HS_dup1393"  
## [277] "L1PA2_dup595"   "L1PA3_dup2954"  "L1PA3_dup6573"  "L1PA2_dup4714" 
## [281] "L1HS_dup1020"   "L1PA2_dup4441"  "L1HS_dup1473"   "L1PA3_dup9202" 
## [285] "L1PA2_dup3405"  "L1PA2_dup4045"  "L1PA2_dup71"    "L1PA3_dup7963" 
## [289] "L1PA2_dup2254"  "L1PA3_dup4391"  "L1PA3_dup10344" "L1HS_dup1514"  
## [293] "L1PA3_dup4401"  "L1PA3_dup247"   "L1PA2_dup365"   "L1PA3_dup7840" 
## [297] "L1PA2_dup1426"  "L1PA2_dup994"   "L1HS_dup1284"   "L1PA3_dup907"  
## [301] "L1PA2_dup1805"  "L1PA3_dup3729"  "L1HS_dup1342"   "L1PA2_dup1049" 
## [305] "L1PA3_dup5468"  "L1PA2_dup4686"  "L1PA2_dup4611"  "L1PA2_dup4522" 
## [309] "L1HS_dup596"    "L1PA2_dup727"   "L1PA2_dup3283"  "L1PA3_dup7237" 
## [313] "L1PA3_dup3307"  "L1HS_dup1019"   "L1PA3_dup4408"  "L1PA2_dup2444" 
## [317] "L1PA2_dup3579"  "L1HS_dup800"    "L1PA2_dup3042"  "L1PA3_dup7472" 
## [321] "L1PA3_dup3959"  "L1HS_dup155"    "L1PA2_dup635"   "L1PA3_dup5510" 
## [325] "L1PA2_dup3445"  "L1PA3_dup7550"  "L1PA2_dup4237"  "L1PA2_dup1177" 
## [329] "L1PA3_dup5544"  "L1HS_dup1077"   "L1PA2_dup326"   "L1PA3_dup4708" 
## [333] "L1HS_dup811"    "L1PA3_dup10096" "L1PA2_dup383"   "L1PA3_dup9856" 
## [337] "L1PA2_dup2295"  "L1PA2_dup4639"  "L1PA3_dup124"   "L1PA2_dup4762" 
## [341] "L1PA2_dup3615"  "L1PA2_dup3930"  "L1PA3_dup6387"  "L1PA2_dup98"   
## [345] "L1HS_dup907"    "L1PA2_dup1058"  "L1PA3_dup2620"  "L1PA2_dup196"  
## [349] "L1PA3_dup3291"  "L1PA2_dup2436"  "L1PA2_dup1746"  "L1HS_dup90"    
## [353] "L1HS_dup803"    "L1PA2_dup4528"  "L1PA2_dup4776"  "L1PA2_dup4367" 
## [357] "L1PA3_dup6160"  "L1PA3_dup3684"  "L1PA2_dup2565"  "L1PA2_dup4378" 
## [361] "L1HS_dup831"    "L1HS_dup1005"   "L1PA3_dup4902"  "L1PA3_dup3509" 
## [365] "L1HS_dup143"    "L1PA2_dup629"   "L1PA3_dup3502"  "L1PA3_dup1463" 
## [369] "L1PA2_dup4309"  "L1PA3_dup6347"  "L1PA2_dup3503"  "L1PA2_dup2988" 
## [373] "L1PA3_dup3507"  "L1PA3_dup2643"  "L1PA3_dup5594"  "L1PA2_dup3439" 
## [377] "L1HS_dup225"    "L1PA2_dup530"   "L1PA3_dup165"   "L1PA2_dup514"  
## [381] "L1PA2_dup382"   "L1PA3_dup1269"  "L1PA3_dup7432"  "L1HS_dup204"   
## [385] "L1PA2_dup732"   "L1PA2_dup4196"  "L1PA2_dup4652"  "L1PA2_dup2271" 
## [389] "L1PA2_dup759"   "L1PA3_dup3880"  "L1PA2_dup3776"  "L1PA3_dup5355" 
## [393] "L1PA3_dup8310"  "L1HS_dup1295"   "L1PA3_dup8328"  "L1PA3_dup1337" 
## [397] "L1PA2_dup413"   "L1PA3_dup5886"  "L1HS_dup679"    "L1PA2_dup2729" 
## [401] "L1PA2_dup684"   "L1PA2_dup1023"  "L1PA2_dup1050"  "L1PA2_dup1272" 
## [405] "L1PA3_dup3300"  "L1PA3_dup5927"  "L1HS_dup87"     "L1HS_dup743"   
## [409] "L1HS_dup1576"   "L1PA3_dup5238"  "L1HS_dup622"    "L1PA3_dup2683" 
## [413] "L1HS_dup1616"   "L1PA2_dup4454"  "L1PA2_dup726"   "L1PA2_dup1968" 
## [417] "L1PA3_dup9998"  "L1PA2_dup4905"  "L1PA2_dup4791"  "L1PA3_dup4688" 
## [421] "L1PA2_dup4618"  "L1HS_dup1437"   "L1PA2_dup2496"  "L1PA2_dup3160" 
## [425] "L1PA2_dup358"   "L1PA2_dup3622"  "L1PA3_dup5057"  "L1PA3_dup1727" 
## [429] "L1PA3_dup1046"  "L1PA3_dup10531" "L1PA2_dup3426"  "L1PA2_dup747"  
## [433] "L1PA3_dup5358"  "L1PA3_dup6966"  "L1PA3_dup1027"  "L1PA3_dup1989" 
## [437] "L1PA3_dup4122"  "L1PA2_dup1978"  "L1PA2_dup219"   "L1PA2_dup1463" 
## [441] "L1PA3_dup6884"  "L1PA3_dup6584"  "L1HS_dup787"    "L1HS_dup802"   
## [445] "L1PA3_dup2039"  "L1PA3_dup3005"  "L1PA3_dup4596"  "L1PA2_dup4478" 
## [449] "L1HS_dup1243"   "L1PA2_dup2876"  "L1PA2_dup2537"  "L1PA3_dup6523" 
## [453] "L1PA2_dup805"   "L1PA3_dup6730"  "L1PA2_dup4201"  "L1PA3_dup7792" 
## [457] "L1PA2_dup2127"  "L1PA3_dup4259"  "L1PA2_dup589"   "L1PA2_dup1248" 
## [461] "L1PA3_dup7316"  "L1PA3_dup5418"  "L1PA2_dup4389"  "L1PA3_dup9840" 
## [465] "L1PA3_dup9722"  "L1PA2_dup2577"  "L1PA3_dup5540"  "L1PA3_dup9866" 
## [469] "L1PA2_dup3003"  "L1PA3_dup8896"  "L1PA3_dup1328"  "L1HS_dup376"   
## [473] "L1PA3_dup3153"  "L1PA2_dup4432"  "L1HS_dup1491"   "L1PA2_dup472"  
## [477] "L1PA2_dup3881"  "L1HS_dup466"    "L1PA2_dup1418"  "L1PA3_dup10176"
## [481] "L1PA2_dup2168"  "L1PA2_dup2089"  "L1PA2_dup2282"  "L1PA3_dup2755" 
## [485] "L1PA2_dup2004"  "L1HS_dup1501"   "L1PA2_dup1078"  "L1PA3_dup5363" 
## [489] "L1PA3_dup638"   "L1PA3_dup7893"  "L1HS_dup600"    "L1PA3_dup6112" 
## [493] "L1PA2_dup2261"  "L1PA3_dup8117"  "L1PA2_dup2581"  "L1PA2_dup3118" 
## [497] "L1PA2_dup3766"  "L1PA3_dup1647"  "L1PA3_dup840"   "L1PA3_dup1279" 
## [501] "L1PA3_dup1952"  "L1PA2_dup3629"  "L1PA3_dup1026"  "L1PA3_dup8313" 
## [505] "L1PA3_dup7288"  "L1PA2_dup798"   "L1PA2_dup2430"  "L1PA2_dup4713" 
## [509] "L1PA2_dup1375"  "L1PA2_dup307"   "L1PA3_dup4687"  "L1PA3_dup5825" 
## [513] "L1PA3_dup1943"  "L1PA2_dup1992"  "L1PA3_dup10043" "L1PA3_dup6871" 
## [517] "L1PA3_dup3950"  "L1PA3_dup683"   "L1PA2_dup4688"  "L1PA3_dup9255"

asap_heatmap_snRNA(region = c("PUT"), 
                   tes = data_TE_annotation[which(data_TE_annotation$type == "L1"),"TE_id"], 
                   return_df = F, 
                   breaks = seq(0,15,length.out = 52), 
                   data = TE_data, 
                   group_cols = c("celltype"), 
                   index_row_reorder = c(L1s_sorted_put),
                   order_cols_groups = order_cols_celltype,
                   title = "PUT L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
                   annotation_cols = annotation_cols)

## $heatmap
## 
## $order_cols
##   [1] "AA_ASAP138_PD_NP16-285_PUT_0"    "AA79_ASAP64_PD_NP16-162_PUT_0"  
##   [3] "AA84_ASAP71_PD_NP19-16_PUT_0"    "AA_ASAP100_ctrl_NP18-148_PUT_0" 
##   [5] "AA_ASAP97_PD_NP21-57_PUT_0"      "AA_ASAP141_ctrl_NP19-218_PUT_0" 
##   [7] "AA87_ASAP76_ctrl_NP18-159_PUT_0" "AA71_ASAP70_PD_NP18-304_PUT_0"  
##   [9] "AA_ASAP98_ctrl_NP16-119_PUT_0"   "AA74_ASAP62_PD_NP16-140_PUT_0"  
##  [11] "AA82_ASAP68_PD_NP18-117_PUT_0"   "AA87_ASAP76_ctrl_NP18-159_PUT_1"
##  [13] "AA_ASAP100_ctrl_NP18-148_PUT_1"  "AA79_ASAP64_PD_NP16-162_PUT_1"  
##  [15] "AA71_ASAP70_PD_NP18-304_PUT_1"   "AA74_ASAP62_PD_NP16-140_PUT_1"  
##  [17] "AA84_ASAP71_PD_NP19-16_PUT_1"    "AA_ASAP139_PD_NP17-232_PUT_1"   
##  [19] "AA_ASAP144_PD_NP19-137_PUT_1"    "AA_ASAP92_ctrl_NP16-284_PUT_1"  
##  [21] "AA_ASAP117_PD_NP22-55_PUT_1"     "AA_ASAP87_PD_NP21-208_PUT_1"    
##  [23] "AA_ASAP88_PD_NP21-217_PUT_1"     "AA89_ASAP78_ctrl_NP19-37_PUT_2" 
##  [25] "AA88_ASAP77_ctrl_NP19-36_PUT_2"  "AA_ASAP96_ctrl_NP18-46_PUT_2"   
##  [27] "AA76_ASAP74_PD_NP19-255_PUT_2"   "AA_ASAP94_ctrl_NP17-20_PUT_2"   
##  [29] "AA86_ASAP73_PD_NP19-108_PUT_2"   "AA_ASAP92_ctrl_NP16-284_PUT_2"  
##  [31] "AA_ASAP146_PD_NP21-04_PUT_2"     "AA_ASAP88_PD_NP21-217_PUT_2"    
##  [33] "AA_ASAP139_PD_NP17-232_PUT_2"    "AA_ASAP93_ctrl_NP16-293_PUT_2"  
##  [35] "AA_ASAP98_ctrl_NP16-119_PUT_2"   "AA_ASAP138_PD_NP16-285_PUT_2"   
##  [37] "AA84_ASAP71_PD_NP19-16_PUT_2"    "AA_ASAP97_PD_NP21-57_PUT_2"     
##  [39] "AA_ASAP87_PD_NP21-208_PUT_2"     "AA74_ASAP62_PD_NP16-140_PUT_2"  
##  [41] "AA71_ASAP70_PD_NP18-304_PUT_2"   "AA85_ASAP72_PD_NP19-23_PUT_2"   
##  [43] "AA73_ASAP65_PD_NP16-269_PUT_2"   "AA82_ASAP68_PD_NP18-117_PUT_2"  
##  [45] "AA77_ASAP61_PD_NP16-25_PUT_2"    "AA79_ASAP64_PD_NP16-162_PUT_2"  
##  [47] "AA_ASAP144_PD_NP19-137_PUT_2"    "AA_ASAP117_PD_NP22-55_PUT_2"    
##  [49] "AA_ASAP100_ctrl_NP18-148_PUT_2"  "AA87_ASAP76_ctrl_NP18-159_PUT_2"
##  [51] "AA83_ASAP69_PD_NP18-287_PUT_2"   "AA81_ASAP67_PD_NP17-191_PUT_2"  
##  [53] "AA_ASAP141_ctrl_NP19-218_PUT_2"  "AA_ASAP140_PD_NP19-91_PUT_2"    
##  [55] "AA_ASAP149_PD_NP23-21_PUT_3"     "AA74_ASAP62_PD_NP16-140_PUT_3"  
##  [57] "AA_ASAP141_ctrl_NP19-218_PUT_3"  "AA84_ASAP71_PD_NP19-16_PUT_3"   
##  [59] "AA79_ASAP64_PD_NP16-162_PUT_3"   "AA_ASAP100_ctrl_NP18-148_PUT_3" 
##  [61] "AA_ASAP144_PD_NP19-137_PUT_3"    "AA_ASAP139_PD_NP17-232_PUT_3"   
##  [63] "AA_ASAP138_PD_NP16-285_PUT_3"    "AA_ASAP117_PD_NP22-55_PUT_3"    
##  [65] "AA_ASAP93_ctrl_NP16-293_PUT_3"   "AA85_ASAP72_PD_NP19-23_PUT_3"   
##  [67] "AA_ASAP140_PD_NP19-91_PUT_3"     "AA86_ASAP73_PD_NP19-108_PUT_3"  
##  [69] "AA_ASAP142_ctrl_NP22-37_PUT_3"   "AA_ASAP94_ctrl_NP17-20_PUT_3"   
##  [71] "AA89_ASAP78_ctrl_NP19-37_PUT_3"  "AA73_ASAP65_PD_NP16-269_PUT_3"  
##  [73] "AA81_ASAP67_PD_NP17-191_PUT_3"   "AA_ASAP146_PD_NP21-04_PUT_3"    
##  [75] "AA76_ASAP74_PD_NP19-255_PUT_3"   "AA_ASAP92_ctrl_NP16-284_PUT_3"  
##  [77] "AA77_ASAP61_PD_NP16-25_PUT_3"    "AA71_ASAP70_PD_NP18-304_PUT_3"  
##  [79] "AA83_ASAP69_PD_NP18-287_PUT_3"   "AA82_ASAP68_PD_NP18-117_PUT_3"  
##  [81] "AA_ASAP88_PD_NP21-217_PUT_3"     "AA88_ASAP77_ctrl_NP19-36_PUT_3" 
##  [83] "AA_ASAP87_PD_NP21-208_PUT_3"     "AA_ASAP97_PD_NP21-57_PUT_3"     
##  [85] "AA87_ASAP76_ctrl_NP18-159_PUT_3" "AA_ASAP98_ctrl_NP16-119_PUT_3"  
##  [87] "AA_ASAP96_ctrl_NP18-46_PUT_3"    "AA_ASAP92_ctrl_NP16-284_PUT_5"  
##  [89] "AA_ASAP146_PD_NP21-04_PUT_5"     "AA_ASAP87_PD_NP21-208_PUT_5"    
##  [91] "AA_ASAP140_PD_NP19-91_PUT_5"     "AA_ASAP141_ctrl_NP19-218_PUT_5" 
##  [93] "AA_ASAP100_ctrl_NP18-148_PUT_5"  "AA_ASAP144_PD_NP19-137_PUT_5"   
##  [95] "AA_ASAP97_PD_NP21-57_PUT_5"      "AA87_ASAP76_ctrl_NP18-159_PUT_5"
##  [97] "AA84_ASAP71_PD_NP19-16_PUT_5"    "AA_ASAP138_PD_NP16-285_PUT_5"   
##  [99] "AA_ASAP139_PD_NP17-232_PUT_5"    "AA_ASAP88_PD_NP21-217_PUT_5"    
## [101] "AA_ASAP98_ctrl_NP16-119_PUT_5"   "AA79_ASAP64_PD_NP16-162_PUT_5"  
## [103] "AA_ASAP117_PD_NP22-55_PUT_5"     "AA_ASAP96_ctrl_NP18-46_PUT_5"   
## [105] "AA71_ASAP70_PD_NP18-304_PUT_5"   "AA86_ASAP73_PD_NP19-108_PUT_5"  
## [107] "AA_ASAP94_ctrl_NP17-20_PUT_5"    "AA89_ASAP78_ctrl_NP19-37_PUT_5" 
## [109] "AA88_ASAP77_ctrl_NP19-36_PUT_5"  "AA85_ASAP72_PD_NP19-23_PUT_5"   
## [111] "AA74_ASAP62_PD_NP16-140_PUT_5"   "AA_ASAP93_ctrl_NP16-293_PUT_5"  
## [113] "AA82_ASAP68_PD_NP18-117_PUT_5"   "AA77_ASAP61_PD_NP16-25_PUT_5"   
## [115] "AA83_ASAP69_PD_NP18-287_PUT_5"   "AA81_ASAP67_PD_NP17-191_PUT_5"  
## [117] "AA73_ASAP65_PD_NP16-269_PUT_5"   "AA_ASAP142_ctrl_NP22-37_PUT_5"  
## [119] "AA76_ASAP74_PD_NP19-255_PUT_5"   "AA_ASAP149_PD_NP23-21_PUT_5"    
## [121] "AA78_ASAP63_PD_NP16-160_PUT_5"   "AA89_ASAP78_ctrl_NP19-37_PUT_4" 
## [123] "AA_ASAP94_ctrl_NP17-20_PUT_4"    "AA_ASAP96_ctrl_NP18-46_PUT_4"   
## [125] "AA_ASAP138_PD_NP16-285_PUT_4"    "AA_ASAP141_ctrl_NP19-218_PUT_4" 
## [127] "AA_ASAP140_PD_NP19-91_PUT_4"     "AA79_ASAP64_PD_NP16-162_PUT_4"  
## [129] "AA73_ASAP65_PD_NP16-269_PUT_4"   "AA85_ASAP72_PD_NP19-23_PUT_4"   
## [131] "AA77_ASAP61_PD_NP16-25_PUT_4"    "AA76_ASAP74_PD_NP19-255_PUT_4"  
## [133] "AA83_ASAP69_PD_NP18-287_PUT_4"   "AA81_ASAP67_PD_NP17-191_PUT_4"  
## [135] "AA74_ASAP62_PD_NP16-140_PUT_4"   "AA71_ASAP70_PD_NP18-304_PUT_4"  
## [137] "AA_ASAP88_PD_NP21-217_PUT_4"     "AA_ASAP87_PD_NP21-208_PUT_4"    
## [139] "AA_ASAP117_PD_NP22-55_PUT_4"     "AA_ASAP97_PD_NP21-57_PUT_4"     
## [141] "AA87_ASAP76_ctrl_NP18-159_PUT_4" "AA_ASAP100_ctrl_NP18-148_PUT_4" 
## [143] "AA_ASAP144_PD_NP19-137_PUT_4"    "AA84_ASAP71_PD_NP19-16_PUT_4"   
## [145] "AA_ASAP98_ctrl_NP16-119_PUT_4"  
## 
## $order_rows
##   [1] "L1PA2_dup791"   "L1PA2_dup848"   "L1PA2_dup1230"  "L1HS_dup1462"  
##   [5] "L1PA3_dup1010"  "L1PA3_dup10686" "L1PA2_dup4403"  "L1PA2_dup585"  
##   [9] "L1PA3_dup398"   "L1HS_dup1324"   "L1HS_dup124"    "L1PA3_dup2557" 
##  [13] "L1PA3_dup8903"  "L1PA3_dup4994"  "L1PA2_dup234"   "L1PA2_dup663"  
##  [17] "L1HS_dup337"    "L1PA2_dup922"   "L1PA3_dup10285" "L1PA2_dup378"  
##  [21] "L1PA3_dup8173"  "L1PA3_dup2744"  "L1PA2_dup949"   "L1PA3_dup10297"
##  [25] "L1PA2_dup4651"  "L1PA2_dup3736"  "L1PA3_dup8420"  "L1PA2_dup4713" 
##  [29] "L1PA3_dup10119" "L1PA2_dup513"   "L1PA2_dup2408"  "L1PA3_dup4492" 
##  [33] "L1PA2_dup2720"  "L1PA2_dup1621"  "L1PA3_dup2413"  "L1PA3_dup2204" 
##  [37] "L1PA2_dup39"    "L1HS_dup455"    "L1PA3_dup2919"  "L1PA3_dup6008" 
##  [41] "L1PA3_dup4888"  "L1PA2_dup526"   "L1PA2_dup927"   "L1PA3_dup1264" 
##  [45] "L1PA2_dup1462"  "L1PA3_dup4118"  "L1PA3_dup4668"  "L1PA3_dup5337" 
##  [49] "L1PA3_dup400"   "L1PA3_dup9095"  "L1PA3_dup1710"  "L1PA2_dup3664" 
##  [53] "L1PA3_dup1651"  "L1PA3_dup2517"  "L1PA3_dup5106"  "L1PA3_dup4277" 
##  [57] "L1HS_dup1014"   "L1PA3_dup1"     "L1PA3_dup872"   "L1PA3_dup2760" 
##  [61] "L1PA3_dup2393"  "L1PA3_dup8522"  "L1PA2_dup2245"  "L1PA3_dup4891" 
##  [65] "L1HS_dup787"    "L1PA2_dup4596"  "L1PA2_dup2680"  "L1PA3_dup9280" 
##  [69] "L1PA3_dup527"   "L1HS_dup916"    "L1PA2_dup559"   "L1PA2_dup3607" 
##  [73] "L1PA3_dup3102"  "L1PA3_dup8663"  "L1PA2_dup2791"  "L1PA3_dup358"  
##  [77] "L1PA2_dup142"   "L1PA3_dup3168"  "L1PA3_dup1800"  "L1PA3_dup3757" 
##  [81] "L1PA2_dup4791"  "L1HS_dup1330"   "L1PA2_dup4237"  "L1PA3_dup1311" 
##  [85] "L1PA3_dup6002"  "L1PA2_dup423"   "L1PA2_dup2343"  "L1PA3_dup761"  
##  [89] "L1PA3_dup1770"  "L1PA3_dup9430"  "L1PA3_dup6385"  "L1PA3_dup8872" 
##  [93] "L1PA2_dup1953"  "L1PA2_dup4620"  "L1PA2_dup2289"  "L1PA2_dup1298" 
##  [97] "L1PA3_dup6884"  "L1PA3_dup10525" "L1PA3_dup8007"  "L1PA2_dup2969" 
## [101] "L1PA2_dup2091"  "L1PA3_dup2593"  "L1PA2_dup4074"  "L1PA3_dup9946" 
## [105] "L1PA2_dup1398"  "L1PA2_dup675"   "L1PA3_dup1547"  "L1PA3_dup5928" 
## [109] "L1PA2_dup662"   "L1PA2_dup727"   "L1PA2_dup1752"  "L1PA3_dup8506" 
## [113] "L1PA3_dup3153"  "L1PA2_dup4936"  "L1PA3_dup1756"  "L1PA3_dup3729" 
## [117] "L1PA3_dup6966"  "L1HS_dup649"    "L1PA3_dup529"   "L1PA3_dup6457" 
## [121] "L1PA2_dup3771"  "L1PA2_dup3425"  "L1HS_dup240"    "L1HS_dup138"   
## [125] "L1PA3_dup9856"  "L1PA3_dup7864"  "L1PA3_dup7470"  "L1PA2_dup2164" 
## [129] "L1PA3_dup5121"  "L1PA3_dup3586"  "L1HS_dup379"    "L1PA3_dup5534" 
## [133] "L1PA2_dup3589"  "L1PA3_dup4709"  "L1PA2_dup3531"  "L1PA2_dup1272" 
## [137] "L1PA2_dup3484"  "L1PA2_dup935"   "L1PA2_dup2909"  "L1PA3_dup6317" 
## [141] "L1HS_dup449"    "L1PA3_dup561"   "L1PA3_dup9021"  "L1PA3_dup1988" 
## [145] "L1PA2_dup4367"  "L1PA3_dup373"   "L1PA2_dup2860"  "L1PA2_dup4053" 
## [149] "L1HS_dup155"    "L1PA2_dup4905"  "L1PA3_dup1428"  "L1PA3_dup4401" 
## [153] "L1PA3_dup10740" "L1HS_dup444"    "L1PA3_dup9473"  "L1PA2_dup3437" 
## [157] "L1PA2_dup3136"  "L1PA3_dup3758"  "L1HS_dup788"    "L1HS_dup1182"  
## [161] "L1PA2_dup2155"  "L1PA2_dup71"    "L1PA3_dup7862"  "L1PA3_dup9256" 
## [165] "L1PA3_dup6036"  "L1PA3_dup683"   "L1PA2_dup1379"  "L1PA3_dup978"  
## [169] "L1HS_dup1339"   "L1PA3_dup6147"  "L1PA2_dup994"   "L1HS_dup596"   
## [173] "L1PA2_dup4639"  "L1PA2_dup2504"  "L1PA2_dup1778"  "L1HS_dup632"   
## [177] "L1PA3_dup3763"  "L1PA2_dup798"   "L1HS_dup1616"   "L1PA2_dup1490" 
## [181] "L1PA2_dup4775"  "L1PA2_dup109"   "L1HS_dup1286"   "L1HS_dup429"   
## [185] "L1PA3_dup7821"  "L1PA3_dup9840"  "L1PA3_dup7605"  "L1PA2_dup2047" 
## [189] "L1HS_dup1536"   "L1PA2_dup3579"  "L1HS_dup111"    "L1PA2_dup4262" 
## [193] "L1PA2_dup2863"  "L1PA3_dup3863"  "L1PA3_dup3507"  "L1HS_dup514"   
## [197] "L1PA2_dup410"   "L1PA3_dup10344" "L1PA3_dup10531" "L1PA3_dup3941" 
## [201] "L1PA3_dup10011" "L1PA3_dup1937"  "L1PA3_dup4885"  "L1PA2_dup3805" 
## [205] "L1PA3_dup165"   "L1PA3_dup5047"  "L1PA3_dup5680"  "L1PA3_dup7951" 
## [209] "L1PA3_dup2272"  "L1PA3_dup1723"  "L1PA3_dup2643"  "L1PA2_dup4548" 
## [213] "L1PA2_dup805"   "L1PA3_dup9734"  "L1PA3_dup4804"  "L1HS_dup1019"  
## [217] "L1PA2_dup4838"  "L1PA2_dup37"    "L1PA2_dup759"   "L1PA3_dup2721" 
## [221] "L1PA3_dup7472"  "L1PA2_dup1426"  "L1PA3_dup5514"  "L1PA3_dup3306" 
## [225] "L1PA2_dup737"   "L1PA2_dup4714"  "L1PA2_dup3292"  "L1PA3_dup128"  
## [229] "L1PA2_dup200"   "L1PA2_dup3615"  "L1PA2_dup4686"  "L1PA2_dup595"  
## [233] "L1PA2_dup1050"  "L1PA2_dup3503"  "L1PA2_dup130"   "L1PA2_dup4196" 
## [237] "L1PA2_dup4762"  "L1PA3_dup3484"  "L1PA3_dup7637"  "L1PA3_dup5510" 
## [241] "L1PA3_dup4688"  "L1PA2_dup4309"  "L1PA2_dup1749"  "L1PA3_dup9373" 
## [245] "L1PA2_dup4901"  "L1PA2_dup2180"  "L1PA3_dup2357"  "L1PA2_dup1968" 
## [249] "L1PA3_dup7237"  "L1PA3_dup6692"  "L1PA2_dup1331"  "L1PA2_dup2254" 
## [253] "L1PA2_dup16"    "L1HS_dup191"    "L1PA2_dup4030"  "L1PA2_dup4440" 
## [257] "L1PA2_dup2261"  "L1PA3_dup8117"  "L1PA3_dup6550"  "L1PA3_dup2551" 
## [261] "L1HS_dup370"    "L1HS_dup995"    "L1PA3_dup6347"  "L1PA3_dup6436" 
## [265] "L1PA2_dup1770"  "L1PA2_dup3405"  "L1HS_dup405"    "L1PA3_dup5363" 
## [269] "L1PA2_dup221"   "L1PA3_dup3968"  "L1PA3_dup8520"  "L1PA3_dup2620" 
## [273] "L1PA3_dup6573"  "L1PA3_dup3954"  "L1HS_dup679"    "L1PA2_dup684"  
## [277] "L1PA3_dup2389"  "L1PA3_dup4902"  "L1PA2_dup3742"  "L1PA2_dup2496" 
## [281] "L1PA3_dup10176" "L1PA2_dup1992"  "L1PA2_dup4421"  "L1PA2_dup4652" 
## [285] "L1PA3_dup3509"  "L1PA2_dup629"   "L1PA3_dup10096" "L1PA3_dup748"  
## [289] "L1HS_dup376"    "L1PA3_dup8328"  "L1PA2_dup635"   "L1PA3_dup1046" 
## [293] "L1PA3_dup9998"  "L1PA3_dup7947"  "L1PA3_dup5355"  "L1PA3_dup3502" 
## [297] "L1HS_dup163"    "L1HS_dup90"     "L1PA2_dup219"   "L1PA3_dup907"  
## [301] "L1PA3_dup8525"  "L1PA2_dup1560"  "L1PA3_dup5468"  "L1PA3_dup5207" 
## [305] "L1HS_dup1393"   "L1PA3_dup8571"  "L1HS_dup35"     "L1PA2_dup1112" 
## [309] "L1HS_dup1478"   "L1HS_dup1295"   "L1HS_dup803"    "L1PA3_dup1989" 
## [313] "L1PA2_dup4430"  "L1PA2_dup4043"  "L1PA3_dup6434"  "L1PA3_dup1952" 
## [317] "L1PA3_dup4708"  "L1HS_dup1243"   "L1PA2_dup2506"  "L1PA3_dup6387" 
## [321] "L1PA2_dup1746"  "L1PA3_dup247"   "L1PA3_dup1528"  "L1PA3_dup6929" 
## [325] "L1PA2_dup3773"  "L1HS_dup1104"   "L1PA3_dup7550"  "L1PA2_dup741"  
## [329] "L1PA3_dup2683"  "L1PA3_dup7963"  "L1PA2_dup360"   "L1HS_dup270"   
## [333] "L1PA2_dup4441"  "L1PA3_dup3950"  "L1PA2_dup358"   "L1PA2_dup98"   
## [337] "L1HS_dup743"    "L1HS_dup811"    "L1PA3_dup2954"  "L1PA3_dup6730" 
## [341] "L1PA2_dup4432"  "L1PA3_dup2039"  "L1PA3_dup1328"  "L1HS_dup579"   
## [345] "L1PA3_dup4487"  "L1PA3_dup124"   "L1PA2_dup2295"  "L1HS_dup204"   
## [349] "L1PA2_dup472"   "L1PA2_dup2004"  "L1PA2_dup747"   "L1HS_dup87"    
## [353] "L1HS_dup1357"   "L1PA2_dup2385"  "L1PA2_dup2444"  "L1PA2_dup4045" 
## [357] "L1PA2_dup3766"  "L1HS_dup1020"   "L1PA2_dup307"   "L1HS_dup466"   
## [361] "L1PA2_dup3042"  "L1PA3_dup4884"  "L1HS_dup244"    "L1PA2_dup3283" 
## [365] "L1PA2_dup4478"  "L1PA2_dup2565"  "L1PA2_dup196"   "L1PA3_dup5745" 
## [369] "L1HS_dup1437"   "L1PA2_dup2436"  "L1PA3_dup7432"  "L1PA2_dup1933" 
## [373] "L1PA3_dup3880"  "L1PA2_dup1078"  "L1PA2_dup1023"  "L1HS_dup1514"  
## [377] "L1PA3_dup2662"  "L1PA3_dup4391"  "L1PA3_dup7840"  "L1PA2_dup413"  
## [381] "L1PA3_dup3300"  "L1HS_dup1077"   "L1PA3_dup8310"  "L1PA2_dup1978" 
## [385] "L1PA2_dup3118"  "L1PA2_dup4522"  "L1HS_dup948"    "L1PA3_dup4603" 
## [389] "L1PA3_dup1554"  "L1PA3_dup4259"  "L1HS_dup1342"   "L1HS_dup879"   
## [393] "L1PA3_dup3684"  "L1PA3_dup7792"  "L1PA2_dup1177"  "L1PA3_dup4596" 
## [397] "L1PA2_dup326"   "L1PA2_dup2271"  "L1PA3_dup4122"  "L1PA2_dup4378" 
## [401] "L1PA2_dup589"   "L1PA3_dup3959"  "L1HS_dup62"     "L1PA2_dup3003" 
## [405] "L1PA3_dup5418"  "L1PA2_dup4776"  "L1PA2_dup1476"  "L1PA2_dup3930" 
## [409] "L1HS_dup907"    "L1PA2_dup3426"  "L1PA3_dup1279"  "L1PA3_dup5866" 
## [413] "L1PA3_dup1027"  "L1PA2_dup4618"  "L1HS_dup1284"   "L1PA2_dup514"  
## [417] "L1PA3_dup1463"  "L1PA2_dup4335"  "L1PA2_dup1248"  "L1PA3_dup4687" 
## [421] "L1PA3_dup5544"  "L1PA2_dup383"   "L1PA2_dup4528"  "L1HS_dup1005"  
## [425] "L1PA2_dup382"   "L1HS_dup800"    "L1HS_dup1576"   "L1PA2_dup2988" 
## [429] "L1HS_dup831"    "L1PA2_dup365"   "L1PA2_dup1049"  "L1PA2_dup2127" 
## [433] "L1PA3_dup1114"  "L1PA2_dup1805"  "L1PA3_dup2755"  "L1PA3_dup8313" 
## [437] "L1PA2_dup1375"  "L1PA2_dup1760"  "L1PA3_dup1550"  "L1PA2_dup3629" 
## [441] "L1PA2_dup726"   "L1PA2_dup2168"  "L1PA3_dup4408"  "L1PA3_dup6160" 
## [445] "L1PA3_dup8891"  "L1PA3_dup7893"  "L1PA2_dup2537"  "L1PA2_dup2577" 
## [449] "L1PA3_dup3323"  "L1PA2_dup4389"  "L1PA2_dup4226"  "L1PA2_dup530"  
## [453] "L1HS_dup143"    "L1HS_dup1473"   "L1PA2_dup1653"  "L1PA2_dup3881" 
## [457] "L1PA3_dup5540"  "L1PA2_dup2089"  "L1PA3_dup6584"  "L1PA3_dup6112" 
## [461] "L1PA2_dup2729"  "L1HS_dup1501"   "L1PA3_dup9702"  "L1PA3_dup4349" 
## [465] "L1PA3_dup840"   "L1PA3_dup5927"  "L1PA2_dup3160"  "L1PA2_dup4454" 
## [469] "L1PA3_dup5358"  "L1PA3_dup3291"  "L1PA2_dup2282"  "L1PA3_dup345"  
## [473] "L1PA2_dup3776"  "L1PA3_dup8896"  "L1HS_dup225"    "L1PA2_dup3439" 
## [477] "L1PA3_dup6871"  "L1PA3_dup3307"  "L1PA3_dup4393"  "L1PA3_dup1647" 
## [481] "L1PA2_dup1058"  "L1HS_dup622"    "L1PA3_dup5238"  "L1PA3_dup1026" 
## [485] "L1PA2_dup3622"  "L1PA2_dup4612"  "L1PA3_dup1269"  "L1PA3_dup1337" 
## [489] "L1PA2_dup732"   "L1PA3_dup6523"  "L1HS_dup1491"   "L1PA3_dup5594" 
## [493] "L1PA2_dup2876"  "L1PA2_dup2430"  "L1PA2_dup3445"  "L1PA2_dup678"  
## [497] "L1HS_dup802"    "L1PA3_dup7316"  "L1PA3_dup638"   "L1PA2_dup2581" 
## [501] "L1HS_dup600"    "L1PA3_dup9255"  "L1PA3_dup10043" "L1PA3_dup5886" 
## [505] "L1PA3_dup10072" "L1PA3_dup3005"  "L1PA3_dup1943"  "L1PA2_dup4611" 
## [509] "L1PA3_dup1727"  "L1PA3_dup9866"  "L1PA3_dup5057"  "L1PA2_dup1418" 
## [513] "L1PA3_dup9202"  "L1PA3_dup7288"  "L1PA2_dup4688"  "L1PA2_dup4201" 
## [517] "L1PA3_dup3404"  "L1PA3_dup9722"  "L1PA2_dup1463"  "L1PA3_dup5825"

asap_heatmap_snRNA(region = c("AMY"), 
                   tes = data_TE_annotation[which(data_TE_annotation$type == "L1"),"TE_id"], 
                   return_df = F, 
                   breaks = seq(0,15,length.out = 52), 
                   data = TE_data, 
                   group_cols = c("celltype"),
                   index_row_reorder = c(L1s_sorted_amy),
                   order_cols_groups = order_cols_celltype,
                   title = "AMY L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
                   annotation_cols = annotation_cols)

## $heatmap
## 
## $order_cols
##   [1] "DA805_ASAP56_ctrl_NP19-37_AMY_0"  "AA_ASAP115_PD_NP21-208_AMY_0"    
##   [3] "AA_ASAP110_ctrl_NP16-119_AMY_0"   "DA474_ASAP24_PD_NP16-25_AMY_0"   
##   [5] "DA811_ASAP18_PD_NP16-140_AMY_0"   "DA780_ASAP37_PD_NP19-16_AMY_0"   
##   [7] "DA793_ASAP53_ctrl_NP19-36_AMY_0"  "DA778_ASAP31_PD_NP18-117_AMY_0"  
##   [9] "DA791_ASAP50_ctrl_NP18-159_AMY_0" "DA783_ASAP45_PD_NP19-255_AMY_0"  
##  [11] "DA802_ASAP40_PD_NP19-23_AMY_0"    "AA_ASAP114_PD_NP21-57_AMY_0"     
##  [13] "AA_ASAP126_PD_NP19-137_AMY_1"     "AA_ASAP128_PD_NP21-04_AMY_1"     
##  [15] "AA_ASAP131_PD_NP23-21_AMY_1"      "AA_ASAP121_PD_NP17-232_AMY_1"    
##  [17] "DA474_ASAP24_PD_NP16-25_AMY_1"    "AA_ASAP110_ctrl_NP16-119_AMY_1"  
##  [19] "AA_ASAP115_PD_NP21-208_AMY_1"     "DA512_ASAP60_ctrl_NP19-45_AMY_1" 
##  [21] "DA805_ASAP56_ctrl_NP19-37_AMY_1"  "AA_ASAP113_ctrl_NP18-148_AMY_1"  
##  [23] "AA_ASAP114_PD_NP21-57_AMY_1"      "AA_ASAP119_PD_NP22-55_AMY_1"     
##  [25] "AA_ASAP123_ctrl_NP19-218_AMY_1"   "AA_ASAP124_ctrl_NP22-37_AMY_1"   
##  [27] "AA_ASAP109_PD_NP21-217_AMY_1"     "DA791_ASAP50_ctrl_NP18-159_AMY_1"
##  [29] "DA778_ASAP31_PD_NP18-117_AMY_1"   "DA793_ASAP53_ctrl_NP19-36_AMY_1" 
##  [31] "DA802_ASAP40_PD_NP19-23_AMY_1"    "DA801_ASAP53_ctrl_NP19-36_AMY_1" 
##  [33] "DA783_ASAP45_PD_NP19-255_AMY_1"   "DA780_ASAP37_PD_NP19-16_AMY_1"   
##  [35] "DA811_ASAP18_PD_NP16-140_AMY_1"   "ASAP122_PD_NP19-91_AMY_2"        
##  [37] "AA_ASAP109_PD_NP21-217_AMY_2"     "AA_ASAP119_PD_NP22-55_AMY_2"     
##  [39] "AA_ASAP126_PD_NP19-137_AMY_2"     "AA_ASAP131_PD_NP23-21_AMY_2"     
##  [41] "DA814_ASAP35_PD_NP18-304_AMY_2"   "AA_ASAP120_PD_NP16-285_AMY_2"    
##  [43] "AA_ASAP128_PD_NP21-04_AMY_2"      "DA783_ASAP45_PD_NP19-255_AMY_2"  
##  [45] "AA_ASAP115_PD_NP21-208_AMY_2"     "DA512_ASAP60_ctrl_NP19-45_AMY_2" 
##  [47] "DA807_ASAP29_PD_NP17-191_AMY_2"   "DA474_ASAP24_PD_NP16-25_AMY_2"   
##  [49] "DA805_ASAP56_ctrl_NP19-37_AMY_2"  "DA811_ASAP18_PD_NP16-140_AMY_2"  
##  [51] "AA_ASAP124_ctrl_NP22-37_AMY_2"    "AA_ASAP121_PD_NP17-232_AMY_2"    
##  [53] "AA_ASAP112_ctrl_NP16-293_AMY_2"   "DA780_ASAP37_PD_NP19-16_AMY_2"   
##  [55] "AA_ASAP123_ctrl_NP19-218_AMY_2"   "AA_ASAP114_PD_NP21-57_AMY_2"     
##  [57] "AA_ASAP110_ctrl_NP16-119_AMY_2"   "AA_ASAP113_ctrl_NP18-148_AMY_2"  
##  [59] "DA791_ASAP50_ctrl_NP18-159_AMY_2" "DA802_ASAP40_PD_NP19-23_AMY_2"   
##  [61] "DA778_ASAP31_PD_NP18-117_AMY_2"   "DA793_ASAP53_ctrl_NP19-36_AMY_2" 
##  [63] "DA801_ASAP53_ctrl_NP19-36_AMY_2"  "DA780_ASAP37_PD_NP19-16_AMY_3"   
##  [65] "DA791_ASAP50_ctrl_NP18-159_AMY_3" "DA778_ASAP31_PD_NP18-117_AMY_3"  
##  [67] "DA803_ASAP48_ctrl_NP17-256_AMY_3" "AA_ASAP131_PD_NP23-21_AMY_3"     
##  [69] "AA_ASAP111_ctrl_NP16-284_AMY_3"   "AA_ASAP115_PD_NP21-208_AMY_3"    
##  [71] "AA_ASAP112_ctrl_NP16-293_AMY_3"   "AA_ASAP120_PD_NP16-285_AMY_3"    
##  [73] "ASAP122_PD_NP19-91_AMY_3"         "DA802_ASAP40_PD_NP19-23_AMY_3"   
##  [75] "DA811_ASAP18_PD_NP16-140_AMY_3"   "AA_ASAP119_PD_NP22-55_AMY_3"     
##  [77] "DA807_ASAP29_PD_NP17-191_AMY_3"   "DA805_ASAP56_ctrl_NP19-37_AMY_3" 
##  [79] "DA474_ASAP24_PD_NP16-25_AMY_3"    "DA793_ASAP53_ctrl_NP19-36_AMY_3" 
##  [81] "DA801_ASAP53_ctrl_NP19-36_AMY_3"  "AA_ASAP123_ctrl_NP19-218_AMY_3"  
##  [83] "AA_ASAP128_PD_NP21-04_AMY_3"      "AA_ASAP110_ctrl_NP16-119_AMY_3"  
##  [85] "AA_ASAP114_PD_NP21-57_AMY_3"      "DA512_ASAP60_ctrl_NP19-45_AMY_3" 
##  [87] "AA_ASAP113_ctrl_NP18-148_AMY_3"   "AA_ASAP124_ctrl_NP22-37_AMY_3"   
##  [89] "DA783_ASAP45_PD_NP19-255_AMY_3"   "AA_ASAP121_PD_NP17-232_AMY_3"    
##  [91] "AA_ASAP109_PD_NP21-217_AMY_3"     "DA800_ASAP20_PD_NP16-160_AMY_5"  
##  [93] "AA_ASAP128_PD_NP21-04_AMY_5"      "AA_ASAP131_PD_NP23-21_AMY_5"     
##  [95] "DA783_ASAP45_PD_NP19-255_AMY_5"   "AA_ASAP110_ctrl_NP16-119_AMY_5"  
##  [97] "AA_ASAP115_PD_NP21-208_AMY_5"     "AA_ASAP126_PD_NP19-137_AMY_5"    
##  [99] "DA512_ASAP60_ctrl_NP19-45_AMY_5"  "DA778_ASAP31_PD_NP18-117_AMY_5"  
## [101] "DA802_ASAP40_PD_NP19-23_AMY_5"    "DA803_ASAP48_ctrl_NP17-256_AMY_5"
## [103] "AA_ASAP120_PD_NP16-285_AMY_5"     "DA779_ASAP33_PD_NP18-287_AMY_5"  
## [105] "DA815_ASAP37_PD_NP19-16_AMY_5"    "DA814_ASAP35_PD_NP18-304_AMY_5"  
## [107] "AA_ASAP121_PD_NP17-232_AMY_5"     "DA811_ASAP18_PD_NP16-140_AMY_5"  
## [109] "DA807_ASAP29_PD_NP17-191_AMY_5"   "DA780_ASAP37_PD_NP19-16_AMY_5"   
## [111] "DA791_ASAP50_ctrl_NP18-159_AMY_5" "AA_ASAP123_ctrl_NP19-218_AMY_5"  
## [113] "AA_ASAP119_PD_NP22-55_AMY_5"      "DA805_ASAP56_ctrl_NP19-37_AMY_5" 
## [115] "DA474_ASAP24_PD_NP16-25_AMY_5"    "AA_ASAP114_PD_NP21-57_AMY_5"     
## [117] "AA_ASAP113_ctrl_NP18-148_AMY_5"   "ASAP122_PD_NP19-91_AMY_5"        
## [119] "AA_ASAP109_PD_NP21-217_AMY_5"     "AA_ASAP124_ctrl_NP22-37_AMY_5"   
## [121] "AA_ASAP112_ctrl_NP16-293_AMY_5"   "DA793_ASAP53_ctrl_NP19-36_AMY_5" 
## [123] "DA801_ASAP53_ctrl_NP19-36_AMY_5"  "AA_ASAP131_PD_NP23-21_AMY_4"     
## [125] "DA512_ASAP60_ctrl_NP19-45_AMY_4"  "AA_ASAP126_PD_NP19-137_AMY_4"    
## [127] "AA_ASAP112_ctrl_NP16-293_AMY_4"   "AA_ASAP115_PD_NP21-208_AMY_4"    
## [129] "DA802_ASAP40_PD_NP19-23_AMY_4"    "DA811_ASAP18_PD_NP16-140_AMY_4"  
## [131] "DA801_ASAP53_ctrl_NP19-36_AMY_4"  "AA_ASAP110_ctrl_NP16-119_AMY_4"  
## [133] "DA793_ASAP53_ctrl_NP19-36_AMY_4"  "DA805_ASAP56_ctrl_NP19-37_AMY_4" 
## [135] "DA474_ASAP24_PD_NP16-25_AMY_4"    "DA807_ASAP29_PD_NP17-191_AMY_4"  
## [137] "AA_ASAP123_ctrl_NP19-218_AMY_4"   "AA_ASAP114_PD_NP21-57_AMY_4"     
## [139] "AA_ASAP113_ctrl_NP18-148_AMY_4"   "DA783_ASAP45_PD_NP19-255_AMY_4"  
## [141] "AA_ASAP119_PD_NP22-55_AMY_4"      "DA791_ASAP50_ctrl_NP18-159_AMY_4"
## [143] "DA778_ASAP31_PD_NP18-117_AMY_4"   "AA_ASAP123_ctrl_NP19-218_AMY_6"  
## 
## $order_rows
##   [1] "L1PA2_dup1230"  "L1PA2_dup848"   "L1PA2_dup791"   "L1HS_dup1462"  
##   [5] "L1PA3_dup398"   "L1PA2_dup4403"  "L1PA2_dup585"   "L1PA2_dup234"  
##   [9] "L1HS_dup337"    "L1PA3_dup1010"  "L1PA3_dup10686" "L1PA2_dup922"  
##  [13] "L1PA3_dup2744"  "L1PA2_dup513"   "L1HS_dup124"    "L1PA2_dup378"  
##  [17] "L1PA3_dup4994"  "L1PA3_dup6385"  "L1HS_dup1324"   "L1PA3_dup2204" 
##  [21] "L1HS_dup455"    "L1PA2_dup663"   "L1PA3_dup8903"  "L1PA3_dup10285"
##  [25] "L1PA2_dup2245"  "L1PA2_dup4651"  "L1PA3_dup8173"  "L1PA3_dup2557" 
##  [29] "L1PA2_dup1462"  "L1PA3_dup1651"  "L1PA2_dup1298"  "L1PA2_dup526"  
##  [33] "L1PA3_dup4492"  "L1PA2_dup949"   "L1PA3_dup2413"  "L1PA3_dup3102" 
##  [37] "L1PA3_dup1"     "L1PA3_dup2919"  "L1PA2_dup3736"  "L1PA3_dup8522" 
##  [41] "L1PA3_dup10297" "L1PA3_dup2593"  "L1PA3_dup761"   "L1PA2_dup1621" 
##  [45] "L1PA3_dup8663"  "L1PA3_dup9946"  "L1PA2_dup927"   "L1PA2_dup4074" 
##  [49] "L1HS_dup916"    "L1PA3_dup7864"  "L1PA3_dup1756"  "L1PA3_dup4118" 
##  [53] "L1PA2_dup3607"  "L1PA3_dup358"   "L1PA3_dup8872"  "L1PA2_dup559"  
##  [57] "L1HS_dup1342"   "L1PA3_dup4709"  "L1PA3_dup9021"  "L1PA2_dup37"   
##  [61] "L1PA2_dup109"   "L1PA3_dup2517"  "L1PA3_dup9095"  "L1PA3_dup872"  
##  [65] "L1PA2_dup2680"  "L1PA2_dup39"    "L1PA2_dup3484"  "L1PA3_dup2760" 
##  [69] "L1PA3_dup10119" "L1PA3_dup400"   "L1PA3_dup1264"  "L1PA2_dup2720" 
##  [73] "L1PA2_dup2504"  "L1PA3_dup1710"  "L1HS_dup1286"   "L1PA2_dup2909" 
##  [77] "L1HS_dup649"    "L1PA3_dup3757"  "L1PA2_dup1953"  "L1HS_dup138"   
##  [81] "L1PA2_dup3664"  "L1PA3_dup6036"  "L1PA2_dup737"   "L1PA2_dup4620" 
##  [85] "L1PA3_dup373"   "L1PA3_dup4891"  "L1PA2_dup727"   "L1PA3_dup8420" 
##  [89] "L1PA3_dup9430"  "L1HS_dup879"    "L1PA3_dup3758"  "L1PA2_dup2180" 
##  [93] "L1PA3_dup5337"  "L1PA2_dup2289"  "L1PA2_dup675"   "L1PA3_dup3168" 
##  [97] "L1PA3_dup10740" "L1PA3_dup7821"  "L1PA3_dup4888"  "L1PA2_dup2091" 
## [101] "L1PA3_dup6002"  "L1PA2_dup3136"  "L1PA2_dup200"   "L1PA2_dup4936" 
## [105] "L1PA2_dup3579"  "L1HS_dup444"    "L1PA3_dup561"   "L1PA3_dup8506" 
## [109] "L1PA3_dup1770"  "L1PA2_dup3425"  "L1PA3_dup4277"  "L1PA3_dup5928" 
## [113] "L1PA3_dup978"   "L1PA2_dup2969"  "L1PA3_dup9702"  "L1PA2_dup3405" 
## [117] "L1PA3_dup1547"  "L1PA2_dup1490"  "L1PA3_dup4603"  "L1PA3_dup3863" 
## [121] "L1PA2_dup3771"  "L1PA3_dup4885"  "L1PA3_dup6147"  "L1PA3_dup4487" 
## [125] "L1PA3_dup2721"  "L1PA2_dup410"   "L1PA3_dup2551"  "L1PA3_dup5514" 
## [129] "L1PA2_dup2408"  "L1PA2_dup2860"  "L1PA2_dup1177"  "L1HS_dup240"   
## [133] "L1PA3_dup529"   "L1PA2_dup130"   "L1PA2_dup3589"  "L1PA3_dup7470" 
## [137] "L1PA2_dup4838"  "L1PA2_dup221"   "L1HS_dup1357"   "L1PA3_dup9280" 
## [141] "L1PA3_dup10525" "L1PA3_dup3586"  "L1PA2_dup3805"  "L1PA3_dup2662" 
## [145] "L1PA3_dup8891"  "L1PA3_dup3300"  "L1PA3_dup527"   "L1PA3_dup1428" 
## [149] "L1PA3_dup7550"  "L1PA3_dup9473"  "L1PA2_dup1272"  "L1PA3_dup2272" 
## [153] "L1PA3_dup6884"  "L1PA3_dup9256"  "L1PA3_dup748"   "L1PA3_dup5121" 
## [157] "L1HS_dup449"    "L1PA2_dup1379"  "L1HS_dup1014"   "L1PA2_dup4548" 
## [161] "L1HS_dup788"    "L1PA2_dup2004"  "L1PA3_dup6457"  "L1PA2_dup3531" 
## [165] "L1PA2_dup4421"  "L1HS_dup1536"   "L1PA2_dup423"   "L1HS_dup596"   
## [169] "L1PA3_dup8525"  "L1PA2_dup1752"  "L1PA2_dup2791"  "L1PA3_dup7951" 
## [173] "L1PA3_dup4884"  "L1PA2_dup759"   "L1PA2_dup595"   "L1HS_dup111"   
## [177] "L1PA2_dup1749"  "L1PA3_dup7605"  "L1PA2_dup684"   "L1HS_dup632"   
## [181] "L1PA3_dup1311"  "L1PA3_dup5680"  "L1PA2_dup3283"  "L1PA3_dup3941" 
## [185] "L1PA2_dup2047"  "L1HS_dup800"    "L1PA2_dup4053"  "L1PA3_dup3306" 
## [189] "L1PA3_dup8571"  "L1PA2_dup3773"  "L1PA2_dup2496"  "L1PA3_dup8007" 
## [193] "L1PA3_dup4668"  "L1PA3_dup8520"  "L1PA3_dup6317"  "L1HS_dup191"   
## [197] "L1PA3_dup9840"  "L1HS_dup35"     "L1PA3_dup247"   "L1PA3_dup10011"
## [201] "L1HS_dup155"    "L1PA2_dup1778"  "L1PA3_dup5594"  "L1PA3_dup6008" 
## [205] "L1PA3_dup2683"  "L1PA2_dup142"   "L1PA3_dup1937"  "L1HS_dup995"   
## [209] "L1PA2_dup2385"  "L1PA3_dup1800"  "L1PA3_dup6692"  "L1HS_dup1330"  
## [213] "L1PA2_dup2863"  "L1PA3_dup1554"  "L1PA2_dup2164"  "L1PA3_dup3763" 
## [217] "L1PA2_dup4454"  "L1PA3_dup3507"  "L1PA2_dup16"    "L1PA3_dup1723" 
## [221] "L1HS_dup429"    "L1PA3_dup8310"  "L1HS_dup1005"   "L1HS_dup1393"  
## [225] "L1PA2_dup382"   "L1PA2_dup1760"  "L1PA2_dup3292"  "L1PA3_dup6573" 
## [229] "L1PA3_dup2643"  "L1PA2_dup2729"  "L1PA3_dup9373"  "L1PA2_dup4441" 
## [233] "L1PA2_dup2988"  "L1PA3_dup6434"  "L1PA2_dup1746"  "L1PA3_dup6929" 
## [237] "L1PA2_dup2254"  "L1PA2_dup2155"  "L1PA3_dup10096" "L1PA3_dup6550" 
## [241] "L1PA2_dup4762"  "L1PA2_dup1049"  "L1PA3_dup5510"  "L1PA2_dup1112" 
## [245] "L1PA2_dup4612"  "L1PA2_dup4686"  "L1HS_dup204"    "L1PA3_dup1988" 
## [249] "L1PA2_dup678"   "L1PA2_dup935"   "L1PA3_dup3954"  "L1PA2_dup4335" 
## [253] "L1HS_dup225"    "L1HS_dup514"    "L1PA2_dup635"   "L1HS_dup1019"  
## [257] "L1PA2_dup3437"  "L1PA2_dup2343"  "L1PA3_dup4401"  "L1PA2_dup1933" 
## [261] "L1HS_dup743"    "L1PA3_dup2954"  "L1PA3_dup7237"  "L1PA2_dup1331" 
## [265] "L1HS_dup379"    "L1PA3_dup165"   "L1PA3_dup1550"  "L1PA2_dup326"  
## [269] "L1PA2_dup4528"  "L1HS_dup948"    "L1PA2_dup662"   "L1PA3_dup907"  
## [273] "L1PA3_dup9734"  "L1HS_dup679"    "L1PA2_dup71"    "L1PA3_dup2039" 
## [277] "L1PA2_dup4596"  "L1PA3_dup2620"  "L1PA3_dup4408"  "L1PA3_dup7963" 
## [281] "L1PA2_dup4045"  "L1PA2_dup4775"  "L1PA3_dup5866"  "L1PA3_dup3484" 
## [285] "L1PA3_dup4804"  "L1PA3_dup4393"  "L1PA3_dup5534"  "L1PA2_dup4030" 
## [289] "L1PA3_dup7862"  "L1PA3_dup7472"  "L1HS_dup1104"   "L1PA3_dup10344"
## [293] "L1PA2_dup365"   "L1HS_dup579"    "L1PA3_dup3502"  "L1PA2_dup4522" 
## [297] "L1PA2_dup2537"  "L1PA3_dup6436"  "L1HS_dup1514"   "L1PA2_dup4714" 
## [301] "L1PA3_dup2393"  "L1PA2_dup1560"  "L1HS_dup62"     "L1PA3_dup3729" 
## [305] "L1HS_dup1182"   "L1PA2_dup1770"  "L1PA2_dup1653"  "L1PA3_dup5544" 
## [309] "L1PA2_dup2282"  "L1PA2_dup3118"  "L1PA3_dup5745"  "L1HS_dup802"   
## [313] "L1PA2_dup4776"  "L1HS_dup622"    "L1PA3_dup3291"  "L1HS_dup1473"  
## [317] "L1HS_dup1478"   "L1PA3_dup6347"  "L1PA3_dup7288"  "L1PA3_dup10176"
## [321] "L1PA3_dup1463"  "L1HS_dup163"    "L1HS_dup811"    "L1PA3_dup9998" 
## [325] "L1PA3_dup7637"  "L1PA3_dup9722"  "L1PA2_dup413"   "L1HS_dup1339"  
## [329] "L1HS_dup466"    "L1PA2_dup2127"  "L1HS_dup370"    "L1HS_dup787"   
## [333] "L1PA3_dup3509"  "L1PA2_dup1398"  "L1PA3_dup8896"  "L1PA3_dup3968" 
## [337] "L1PA3_dup1114"  "L1PA2_dup805"   "L1PA2_dup747"   "L1PA3_dup3404" 
## [341] "L1PA3_dup2357"  "L1PA3_dup6387"  "L1PA2_dup472"   "L1PA3_dup4391" 
## [345] "L1PA3_dup3307"  "L1PA2_dup307"   "L1PA2_dup2436"  "L1HS_dup803"   
## [349] "L1PA3_dup5106"  "L1PA3_dup7947"  "L1PA3_dup3323"  "L1PA2_dup514"  
## [353] "L1HS_dup270"    "L1HS_dup1576"   "L1PA2_dup4478"  "L1PA3_dup2389" 
## [357] "L1PA3_dup4122"  "L1PA2_dup994"   "L1PA3_dup8313"  "L1PA2_dup3881" 
## [361] "L1PA2_dup2444"  "L1HS_dup244"    "L1PA2_dup2089"  "L1PA3_dup5468" 
## [365] "L1HS_dup1077"   "L1PA2_dup1023"  "L1PA3_dup2755"  "L1PA3_dup3880" 
## [369] "L1PA3_dup5355"  "L1PA2_dup1050"  "L1HS_dup405"    "L1PA3_dup6730" 
## [373] "L1PA2_dup1248"  "L1HS_dup831"    "L1PA2_dup3615"  "L1PA2_dup3622" 
## [377] "L1PA3_dup4259"  "L1HS_dup1437"   "L1PA3_dup683"   "L1PA3_dup4708" 
## [381] "L1PA2_dup2581"  "L1PA3_dup8117"  "L1PA2_dup4618"  "L1PA3_dup7840" 
## [385] "L1PA2_dup4430"  "L1PA3_dup124"   "L1PA2_dup4440"  "L1HS_dup376"   
## [389] "L1PA3_dup128"   "L1PA3_dup8328"  "L1PA2_dup2506"  "L1PA3_dup4688" 
## [393] "L1PA2_dup1426"  "L1PA2_dup3042"  "L1PA2_dup4389"  "L1HS_dup1020"  
## [397] "L1PA2_dup1992"  "L1PA2_dup4262"  "L1PA3_dup5238"  "L1PA3_dup5886" 
## [401] "L1PA3_dup6112"  "L1PA3_dup7893"  "L1PA3_dup5927"  "L1PA3_dup6160" 
## [405] "L1PA2_dup4652"  "L1PA3_dup6966"  "L1PA2_dup1805"  "L1PA2_dup629"  
## [409] "L1PA2_dup741"   "L1PA2_dup2577"  "L1PA3_dup7432"  "L1PA2_dup4639" 
## [413] "L1PA2_dup196"   "L1PA3_dup10072" "L1PA3_dup10043" "L1PA3_dup840"  
## [417] "L1PA2_dup4196"  "L1PA2_dup530"   "L1PA2_dup2295"  "L1PA3_dup5207" 
## [421] "L1PA3_dup3684"  "L1PA2_dup798"   "L1PA2_dup2271"  "L1PA2_dup4791" 
## [425] "L1HS_dup1284"   "L1PA2_dup2876"  "L1PA2_dup3003"  "L1PA3_dup1328" 
## [429] "L1PA2_dup726"   "L1PA2_dup3742"  "L1PA3_dup1528"  "L1PA2_dup4432" 
## [433] "L1PA2_dup4901"  "L1PA3_dup1989"  "L1PA2_dup1463"  "L1PA2_dup4043" 
## [437] "L1HS_dup87"     "L1PA2_dup1978"  "L1PA2_dup3445"  "L1HS_dup90"    
## [441] "L1PA2_dup4237"  "L1PA2_dup4611"  "L1HS_dup1616"   "L1PA3_dup9866" 
## [445] "L1PA3_dup3153"  "L1HS_dup1501"   "L1PA2_dup219"   "L1PA3_dup6584" 
## [449] "L1PA3_dup4349"  "L1PA2_dup4367"  "L1PA3_dup1269"  "L1PA3_dup3959" 
## [453] "L1PA2_dup4309"  "L1PA2_dup3503"  "L1PA2_dup358"   "L1PA3_dup4902" 
## [457] "L1HS_dup143"    "L1PA2_dup4905"  "L1PA3_dup5358"  "L1PA3_dup5047" 
## [461] "L1PA3_dup5363"  "L1PA3_dup1046"  "L1PA2_dup360"   "L1PA2_dup1476" 
## [465] "L1PA3_dup1027"  "L1PA2_dup3426"  "L1HS_dup1243"   "L1PA2_dup4378" 
## [469] "L1PA3_dup9856"  "L1PA3_dup1026"  "L1PA3_dup5825"  "L1PA3_dup638"  
## [473] "L1PA3_dup7792"  "L1PA3_dup4596"  "L1PA3_dup1952"  "L1PA2_dup3160" 
## [477] "L1PA3_dup345"   "L1PA2_dup1375"  "L1PA2_dup3439"  "L1PA3_dup10531"
## [481] "L1PA3_dup9255"  "L1PA2_dup2168"  "L1PA3_dup9202"  "L1HS_dup907"   
## [485] "L1PA3_dup1727"  "L1PA2_dup2565"  "L1HS_dup1491"   "L1PA3_dup1279" 
## [489] "L1PA2_dup383"   "L1PA2_dup3930"  "L1PA2_dup1058"  "L1PA3_dup3005" 
## [493] "L1PA2_dup4201"  "L1PA3_dup5418"  "L1PA2_dup2430"  "L1PA3_dup7316" 
## [497] "L1PA2_dup3766"  "L1PA3_dup5540"  "L1PA2_dup589"   "L1PA3_dup1647" 
## [501] "L1PA2_dup3776"  "L1PA2_dup4713"  "L1PA2_dup3629"  "L1PA2_dup732"  
## [505] "L1PA2_dup1968"  "L1PA3_dup4687"  "L1PA2_dup1418"  "L1PA3_dup3950" 
## [509] "L1PA2_dup98"    "L1PA3_dup1337"  "L1HS_dup600"    "L1PA3_dup5057" 
## [513] "L1PA3_dup6871"  "L1HS_dup1295"   "L1PA2_dup1078"  "L1PA2_dup4226" 
## [517] "L1PA3_dup1943"  "L1PA3_dup6523"  "L1PA2_dup2261"  "L1PA2_dup4688"

asap_heatmap_snRNA(region = c("SN"), 
                   tes = data_TE_annotation[which(data_TE_annotation$type == "L1"),"TE_id"], 
                   return_df = F, 
                   breaks = seq(0,15,length.out = 52), 
                   data = TE_data, 
                   group_cols = c("celltype"), 
                   index_row_reorder = c(L1s_sorted_sn),
                   order_cols_groups = order_cols_celltype,
                   title = "SN L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
                   annotation_cols = annotation_cols)

## $heatmap
## 
## $order_cols
##   [1] "AA_ASAP129_ctrl_NP22-37_SN_1"    "AA_ASAP118_PD_NP22-55_SN_1"     
##   [3] "DA792_ASAP51_ctrl_NP19-36_SN_1"  "AA_ASAP137_PD_NP23-21_SN_1"     
##   [5] "DA487_ASAP8_ctrl_PT231_SN_1"     "DA479_ASAP7_ctrl_NP16-21_SN_2"  
##   [7] "DA487_ASAP8_ctrl_PT231_SN_2"     "AA_ASAP127_ctrl_NP19-218_SN_2"  
##   [9] "AA_ASAP108_ctrl_NP18-148_SN_2"   "DA433_ASAP5_ctrl_NP16-161_SN_2" 
##  [11] "AA_ASAP99_ctrl_NP16-284_SN_2"    "DA431_ASAP4_PD_P74_SN_2"        
##  [13] "DA782_ASAP41_PD_NP19-108_SN_2"   "AA_ASAP129_ctrl_NP22-37_SN_2"   
##  [15] "AA_ASAP118_PD_NP22-55_SN_2"      "DA784_ASAP46_ctrl_NP17-256_SN_2"
##  [17] "DA475_ASAP2_PD_NP16-25_SN_2"     "AA_ASAP133_PD_NP17-232_SN_2"    
##  [19] "MJ_ASAP6_ctrl_NP16-164_SN_2"     "AA_ASAP137_PD_NP23-21_SN_2"     
##  [21] "DA792_ASAP51_ctrl_NP19-36_SN_2"  "AA_ASAP135_PD_NP19-137_SN_2"    
##  [23] "DA794_ASAP54_ctrl_NP19-37_SN_2"  "AA_ASAP101_PD_NP21-57_SN_2"     
##  [25] "DA489_ASAP3_PD_P73_SN_2"         "AA_ASAP103_PD_NP21-217_SN_2"    
##  [27] "AA_ASAP102_PD_NP21-208_SN_2"     "DA429_ASAP1_PD_NP16-162_SN_2"   
##  [29] "DA473_ASAP38_PD_NP19-23_SN_2"    "AA_ASAP105_ctrl_NP16-293_SN_2"  
##  [31] "DA511_ASAP21_PD_NP16-269_SN_2"   "AA_ASAP134_PD_NP19-91_SN_2"     
##  [33] "AA_ASAP104_ctrl_NP16-119_SN_2"   "AA_ASAP132_PD_NP16-285_SN_2"    
##  [35] "DA796_ASAP57_ctrl_NP19-45_SN_2"  "MJ_ASAP6_ctrl_NP16-164_SN_3"    
##  [37] "AA_ASAP129_ctrl_NP22-37_SN_3"    "DA489_ASAP3_PD_P73_SN_3"        
##  [39] "DA475_ASAP2_PD_NP16-25_SN_3"     "DA433_ASAP5_ctrl_NP16-161_SN_3" 
##  [41] "DA479_ASAP7_ctrl_NP16-21_SN_3"   "DA431_ASAP4_PD_P74_SN_3"        
##  [43] "AA_ASAP133_PD_NP17-232_SN_3"     "AA_ASAP137_PD_NP23-21_SN_3"     
##  [45] "AA_ASAP135_PD_NP19-137_SN_3"     "AA_ASAP127_ctrl_NP19-218_SN_3"  
##  [47] "AA_ASAP103_PD_NP21-217_SN_3"     "DA511_ASAP21_PD_NP16-269_SN_3"  
##  [49] "AA_ASAP101_PD_NP21-57_SN_3"      "AA_ASAP102_PD_NP21-208_SN_3"    
##  [51] "AA_ASAP136_PD_NP21-04_SN_3"      "AA_ASAP132_PD_NP16-285_SN_3"    
##  [53] "AA_ASAP99_ctrl_NP16-284_SN_3"    "AA_ASAP104_ctrl_NP16-119_SN_3"  
##  [55] "DA782_ASAP41_PD_NP19-108_SN_3"   "AA_ASAP134_PD_NP19-91_SN_3"     
##  [57] "AA_ASAP118_PD_NP22-55_SN_3"      "DA796_ASAP57_ctrl_NP19-45_SN_3" 
##  [59] "DA784_ASAP46_ctrl_NP17-256_SN_3" "DA487_ASAP8_ctrl_PT231_SN_3"    
##  [61] "DA473_ASAP38_PD_NP19-23_SN_3"    "AA_ASAP105_ctrl_NP16-293_SN_3"  
##  [63] "AA_ASAP108_ctrl_NP18-148_SN_3"   "DA429_ASAP1_PD_NP16-162_SN_3"   
##  [65] "DA794_ASAP54_ctrl_NP19-37_SN_3"  "DA792_ASAP51_ctrl_NP19-36_SN_3" 
##  [67] "MJ_ASAP6_ctrl_NP16-164_SN_5"     "AA_ASAP129_ctrl_NP22-37_SN_5"   
##  [69] "DA489_ASAP3_PD_P73_SN_5"         "AA_ASAP136_PD_NP21-04_SN_5"     
##  [71] "AA_ASAP132_PD_NP16-285_SN_5"     "DA784_ASAP46_ctrl_NP17-256_SN_5"
##  [73] "DA487_ASAP8_ctrl_PT231_SN_5"     "AA_ASAP105_ctrl_NP16-293_SN_5"  
##  [75] "AA_ASAP118_PD_NP22-55_SN_5"      "AA_ASAP137_PD_NP23-21_SN_5"     
##  [77] "AA_ASAP127_ctrl_NP19-218_SN_5"   "DA511_ASAP21_PD_NP16-269_SN_5"  
##  [79] "DA475_ASAP2_PD_NP16-25_SN_5"     "AA_ASAP135_PD_NP19-137_SN_5"    
##  [81] "DA473_ASAP38_PD_NP19-23_SN_5"    "DA431_ASAP4_PD_P74_SN_5"        
##  [83] "DA433_ASAP5_ctrl_NP16-161_SN_5"  "AA_ASAP101_PD_NP21-57_SN_5"     
##  [85] "AA_ASAP103_PD_NP21-217_SN_5"     "AA_ASAP104_ctrl_NP16-119_SN_5"  
##  [87] "AA_ASAP108_ctrl_NP18-148_SN_5"   "DA794_ASAP54_ctrl_NP19-37_SN_5" 
##  [89] "AA_ASAP102_PD_NP21-208_SN_5"     "AA_ASAP99_ctrl_NP16-284_SN_5"   
##  [91] "DA429_ASAP1_PD_NP16-162_SN_5"    "DA479_ASAP7_ctrl_NP16-21_SN_5"  
##  [93] "AA_ASAP133_PD_NP17-232_SN_5"     "AA_ASAP134_PD_NP19-91_SN_5"     
##  [95] "DA782_ASAP41_PD_NP19-108_SN_5"   "DA792_ASAP51_ctrl_NP19-36_SN_5" 
##  [97] "DA796_ASAP57_ctrl_NP19-45_SN_5"  "AA_ASAP134_PD_NP19-91_SN_4"     
##  [99] "DA431_ASAP4_PD_P74_SN_4"         "AA_ASAP129_ctrl_NP22-37_SN_4"   
## [101] "DA487_ASAP8_ctrl_PT231_SN_4"     "DA433_ASAP5_ctrl_NP16-161_SN_4" 
## [103] "DA475_ASAP2_PD_NP16-25_SN_4"     "AA_ASAP137_PD_NP23-21_SN_4"     
## [105] "DA473_ASAP38_PD_NP19-23_SN_4"    "AA_ASAP104_ctrl_NP16-119_SN_4"  
## [107] "DA511_ASAP21_PD_NP16-269_SN_4"   "DA489_ASAP3_PD_P73_SN_4"        
## [109] "AA_ASAP127_ctrl_NP19-218_SN_4"   "AA_ASAP101_PD_NP21-57_SN_4"     
## [111] "DA792_ASAP51_ctrl_NP19-36_SN_4"  "DA794_ASAP54_ctrl_NP19-37_SN_4" 
## [113] "AA_ASAP133_PD_NP17-232_SN_4"     "AA_ASAP118_PD_NP22-55_SN_4"     
## [115] "AA_ASAP103_PD_NP21-217_SN_4"     "AA_ASAP135_PD_NP19-137_SN_4"    
## [117] "DA782_ASAP41_PD_NP19-108_SN_4"   "AA_ASAP102_PD_NP21-208_SN_4"    
## [119] "AA_ASAP108_ctrl_NP18-148_SN_4"   "MJ_ASAP6_ctrl_NP16-164_SN_4"    
## [121] "DA429_ASAP1_PD_NP16-162_SN_4"    "AA_ASAP137_PD_NP23-21_SN_6"     
## [123] "DA792_ASAP51_ctrl_NP19-36_SN_6"  "AA_ASAP133_PD_NP17-232_SN_7"    
## [125] "AA_ASAP137_PD_NP23-21_SN_7"      "AA_ASAP108_ctrl_NP18-148_SN_7"  
## 
## $order_rows
##   [1] "L1PA2_dup791"   "L1PA2_dup1230"  "L1PA2_dup848"   "L1PA3_dup398"  
##   [5] "L1PA2_dup4403"  "L1HS_dup1462"   "L1PA3_dup7864"  "L1PA3_dup529"  
##   [9] "L1PA2_dup234"   "L1PA2_dup585"   "L1PA3_dup4994"  "L1PA2_dup1933" 
##  [13] "L1HS_dup337"    "L1PA2_dup922"   "L1PA3_dup10686" "L1PA2_dup513"  
##  [17] "L1PA3_dup1010"  "L1PA2_dup4905"  "L1HS_dup455"    "L1PA3_dup1651" 
##  [21] "L1PA3_dup8903"  "L1PA3_dup2744"  "L1PA2_dup3736"  "L1PA3_dup2557" 
##  [25] "L1PA3_dup358"   "L1PA3_dup10285" "L1PA3_dup8872"  "L1PA3_dup6385" 
##  [29] "L1PA2_dup663"   "L1PA3_dup1"     "L1PA2_dup2720"  "L1PA3_dup10297"
##  [33] "L1PA3_dup3102"  "L1PA3_dup761"   "L1PA3_dup3757"  "L1PA3_dup10119"
##  [37] "L1PA3_dup8522"  "L1PA2_dup4548"  "L1PA3_dup400"   "L1PA2_dup3405" 
##  [41] "L1PA2_dup559"   "L1PA2_dup1462"  "L1PA2_dup526"   "L1PA2_dup927"  
##  [45] "L1PA3_dup2413"  "L1PA3_dup4709"  "L1PA2_dup37"    "L1PA3_dup2204" 
##  [49] "L1PA3_dup8173"  "L1PA3_dup872"   "L1PA2_dup4651"  "L1PA2_dup4309" 
##  [53] "L1PA2_dup949"   "L1PA2_dup39"    "L1PA3_dup9256"  "L1PA3_dup5358" 
##  [57] "L1PA2_dup4528"  "L1HS_dup1536"   "L1PA3_dup9430"  "L1PA3_dup1710" 
##  [61] "L1PA2_dup2245"  "L1PA2_dup200"   "L1PA2_dup675"   "L1PA3_dup3323" 
##  [65] "L1PA2_dup423"   "L1PA3_dup4118"  "L1PA2_dup16"    "L1PA2_dup378"  
##  [69] "L1PA3_dup4891"  "L1PA3_dup373"   "L1PA3_dup2919"  "L1PA3_dup10740"
##  [73] "L1PA3_dup1756"  "L1PA2_dup3607"  "L1PA2_dup142"   "L1PA3_dup7472" 
##  [77] "L1PA2_dup1298"  "L1PA3_dup8663"  "L1PA2_dup3589"  "L1PA2_dup4620" 
##  [81] "L1PA3_dup3758"  "L1PA2_dup1379"  "L1PA3_dup2517"  "L1PA3_dup2760" 
##  [85] "L1PA3_dup4804"  "L1PA3_dup7470"  "L1PA2_dup1621"  "L1PA2_dup2680" 
##  [89] "L1PA3_dup6002"  "L1HS_dup1576"   "L1PA2_dup2289"  "L1PA2_dup2565" 
##  [93] "L1HS_dup1324"   "L1PA3_dup6036"  "L1PA3_dup8506"  "L1PA2_dup3805" 
##  [97] "L1PA3_dup7862"  "L1PA2_dup4030"  "L1PA3_dup5928"  "L1PA2_dup741"  
## [101] "L1PA2_dup3484"  "L1PA3_dup4888"  "L1PA2_dup3771"  "L1HS_dup1182"  
## [105] "L1PA2_dup4686"  "L1PA2_dup3118"  "L1PA3_dup2551"  "L1PA2_dup2969" 
## [109] "L1PA3_dup9473"  "L1PA2_dup1752"  "L1HS_dup1330"   "L1PA3_dup1800" 
## [113] "L1PA2_dup2791"  "L1PA3_dup8571"  "L1PA2_dup410"   "L1PA3_dup9095" 
## [117] "L1PA2_dup1778"  "L1PA3_dup3168"  "L1PA3_dup2393"  "L1HS_dup995"   
## [121] "L1PA3_dup5121"  "L1PA3_dup4885"  "L1PA2_dup727"   "L1PA2_dup2506" 
## [125] "L1PA2_dup2909"  "L1HS_dup632"    "L1PA3_dup6317"  "L1PA2_dup4688" 
## [129] "L1PA2_dup221"   "L1PA3_dup1547"  "L1PA3_dup1311"  "L1PA3_dup3586" 
## [133] "L1PA2_dup1953"  "L1PA3_dup5106"  "L1PA3_dup9998"  "L1HS_dup800"   
## [137] "L1HS_dup514"    "L1PA3_dup10525" "L1PA3_dup4487"  "L1PA3_dup5680" 
## [141] "L1HS_dup240"    "L1PA3_dup1937"  "L1PA3_dup4277"  "L1PA3_dup5514" 
## [145] "L1PA3_dup6147"  "L1HS_dup879"    "L1PA3_dup527"   "L1PA2_dup4618" 
## [149] "L1PA3_dup2593"  "L1HS_dup649"    "L1HS_dup1014"   "L1PA2_dup3664" 
## [153] "L1HS_dup1473"   "L1HS_dup376"    "L1PA2_dup662"   "L1PA2_dup4762" 
## [157] "L1PA3_dup8007"  "L1PA3_dup5534"  "L1PA3_dup1428"  "L1PA3_dup9280" 
## [161] "L1PA3_dup5337"  "L1PA3_dup4687"  "L1PA2_dup1490"  "L1PA3_dup4492" 
## [165] "L1PA2_dup2164"  "L1PA3_dup3684"  "L1HS_dup191"    "L1HS_dup788"   
## [169] "L1PA3_dup3307"  "L1PA2_dup4440"  "L1PA2_dup2343"  "L1PA2_dup2860" 
## [173] "L1PA3_dup7550"  "L1PA3_dup1264"  "L1PA3_dup7821"  "L1PA3_dup128"  
## [177] "L1PA2_dup1749"  "L1PA3_dup4401"  "L1PA2_dup4074"  "L1PA3_dup7963" 
## [181] "L1PA3_dup6457"  "L1HS_dup1005"   "L1PA3_dup4902"  "L1PA3_dup9021" 
## [185] "L1HS_dup379"    "L1PA2_dup737"   "L1PA3_dup3968"  "L1PA3_dup1723" 
## [189] "L1PA2_dup71"    "L1PA2_dup130"   "L1PA2_dup4936"  "L1PA3_dup4884" 
## [193] "L1PA2_dup2155"  "L1PA2_dup4596"  "L1HS_dup444"    "L1HS_dup1286"  
## [197] "L1PA2_dup2091"  "L1PA3_dup978"   "L1HS_dup155"    "L1PA3_dup2721" 
## [201] "L1PA2_dup726"   "L1HS_dup124"    "L1PA3_dup561"   "L1PA2_dup2385" 
## [205] "L1PA3_dup9840"  "L1HS_dup916"    "L1PA2_dup1272"  "L1PA2_dup1476" 
## [209] "L1PA3_dup907"   "L1PA3_dup1989"  "L1PA2_dup1770"  "L1PA3_dup6692" 
## [213] "L1PA2_dup219"   "L1PA2_dup935"   "L1PA3_dup1554"  "L1PA2_dup3136" 
## [217] "L1PA2_dup589"   "L1PA3_dup6347"  "L1PA3_dup3300"  "L1PA3_dup8420" 
## [221] "L1PA2_dup2180"  "L1HS_dup948"    "L1PA2_dup2863"  "L1PA2_dup1746" 
## [225] "L1PA3_dup7951"  "L1PA3_dup3306"  "L1PA3_dup3502"  "L1PA3_dup5745" 
## [229] "L1PA2_dup109"   "L1PA2_dup595"   "L1PA3_dup3763"  "L1PA3_dup8525" 
## [233] "L1PA3_dup1269"  "L1PA2_dup4522"  "L1PA3_dup10344" "L1PA2_dup3776" 
## [237] "L1HS_dup111"    "L1PA2_dup3437"  "L1PA2_dup994"   "L1PA2_dup382"  
## [241] "L1HS_dup1393"   "L1PA2_dup1398"  "L1PA3_dup2357"  "L1PA3_dup6008" 
## [245] "L1PA3_dup6550"  "L1PA3_dup5544"  "L1PA2_dup1805"  "L1PA2_dup3531" 
## [249] "L1PA3_dup124"   "L1PA3_dup3941"  "L1PA3_dup2954"  "L1PA3_dup4668" 
## [253] "L1PA2_dup3292"  "L1HS_dup449"    "L1PA2_dup4196"  "L1PA3_dup1528" 
## [257] "L1PA2_dup2168"  "L1PA3_dup4708"  "L1PA2_dup2436"  "L1PA3_dup5468" 
## [261] "L1PA3_dup9856"  "L1PA3_dup10176" "L1PA2_dup3615"  "L1PA3_dup2272" 
## [265] "L1PA3_dup6584"  "L1PA2_dup4714"  "L1PA3_dup6573"  "L1PA3_dup165"  
## [269] "L1HS_dup787"    "L1PA3_dup7893"  "L1PA2_dup530"   "L1PA3_dup5866" 
## [273] "L1PA2_dup2408"  "L1HS_dup831"    "L1PA3_dup2620"  "L1HS_dup270"   
## [277] "L1PA3_dup1952"  "L1PA2_dup3742"  "L1PA2_dup4791"  "L1PA3_dup4688" 
## [281] "L1HS_dup244"    "L1HS_dup35"     "L1PA2_dup2988"  "L1PA2_dup635"  
## [285] "L1PA3_dup4122"  "L1PA2_dup3439"  "L1PA3_dup9255"  "L1PA3_dup3507" 
## [289] "L1PA2_dup1968"  "L1PA3_dup3954"  "L1PA2_dup759"   "L1PA2_dup4775" 
## [293] "L1PA3_dup6434"  "L1PA2_dup1049"  "L1HS_dup1077"   "L1PA2_dup2271" 
## [297] "L1HS_dup138"    "L1PA3_dup1943"  "L1PA3_dup9734"  "L1PA3_dup3509" 
## [301] "L1PA3_dup5594"  "L1HS_dup1339"   "L1PA3_dup7237"  "L1PA2_dup3579" 
## [305] "L1PA2_dup2127"  "L1PA2_dup1560"  "L1PA3_dup5207"  "L1PA2_dup3881" 
## [309] "L1PA3_dup748"   "L1HS_dup429"    "L1PA3_dup1279"  "L1HS_dup1478"  
## [313] "L1PA3_dup2389"  "L1HS_dup679"    "L1PA2_dup1426"  "L1PA3_dup5418" 
## [317] "L1PA2_dup1331"  "L1PA3_dup2662"  "L1PA3_dup4603"  "L1PA2_dup4053" 
## [321] "L1PA3_dup4259"  "L1PA3_dup10011" "L1PA2_dup747"   "L1HS_dup1342"  
## [325] "L1PA2_dup1375"  "L1PA2_dup1418"  "L1PA2_dup4901"  "L1PA2_dup3773" 
## [329] "L1PA3_dup1770"  "L1PA2_dup4652"  "L1HS_dup1357"   "L1PA3_dup4349" 
## [333] "L1PA3_dup2683"  "L1HS_dup143"    "L1HS_dup1437"   "L1PA3_dup345"  
## [337] "L1PA2_dup4838"  "L1PA2_dup1050"  "L1PA3_dup6387"  "L1PA3_dup9373" 
## [341] "L1PA2_dup472"   "L1PA3_dup10096" "L1PA2_dup326"   "L1PA2_dup3622" 
## [345] "L1PA3_dup1550"  "L1HS_dup87"     "L1PA3_dup3153"  "L1PA2_dup3629" 
## [349] "L1PA2_dup3425"  "L1PA3_dup10043" "L1PA2_dup1978"  "L1HS_dup405"   
## [353] "L1PA3_dup3005"  "L1PA2_dup4639"  "L1PA2_dup2295"  "L1PA2_dup4421" 
## [357] "L1PA2_dup4262"  "L1HS_dup1020"   "L1PA3_dup5047"  "L1PA2_dup360"  
## [361] "L1HS_dup743"    "L1PA2_dup1760"  "L1PA3_dup10072" "L1PA3_dup8328" 
## [365] "L1PA3_dup3863"  "L1PA2_dup4378"  "L1HS_dup466"    "L1PA3_dup5540" 
## [369] "L1PA3_dup638"   "L1HS_dup1104"   "L1HS_dup90"     "L1PA2_dup358"  
## [373] "L1PA2_dup4237"  "L1HS_dup225"    "L1PA3_dup5355"  "L1PA2_dup629"  
## [377] "L1PA2_dup196"   "L1PA3_dup6929"  "L1PA2_dup2430"  "L1PA2_dup2444" 
## [381] "L1PA2_dup4776"  "L1HS_dup907"    "L1PA3_dup8891"  "L1PA2_dup3445" 
## [385] "L1PA2_dup2537"  "L1PA2_dup4201"  "L1HS_dup204"    "L1PA2_dup2496" 
## [389] "L1PA3_dup6436"  "L1HS_dup1243"   "L1PA2_dup2047"  "L1PA2_dup1177" 
## [393] "L1HS_dup1491"   "L1PA3_dup8310"  "L1PA3_dup7637"  "L1PA3_dup7432" 
## [397] "L1PA2_dup4441"  "L1PA3_dup9702"  "L1PA2_dup2282"  "L1PA3_dup9946" 
## [401] "L1PA3_dup7792"  "L1HS_dup163"    "L1PA3_dup3404"  "L1PA2_dup805"  
## [405] "L1HS_dup600"    "L1HS_dup1019"   "L1PA2_dup4045"  "L1PA2_dup732"  
## [409] "L1PA2_dup4335"  "L1PA3_dup1727"  "L1PA3_dup6966"  "L1PA3_dup9202" 
## [413] "L1PA3_dup3959"  "L1PA3_dup1988"  "L1HS_dup596"    "L1PA3_dup7947" 
## [417] "L1PA2_dup3042"  "L1PA3_dup4391"  "L1PA2_dup3283"  "L1PA2_dup1078" 
## [421] "L1PA2_dup2581"  "L1PA2_dup4478"  "L1PA2_dup413"   "L1PA3_dup1647" 
## [425] "L1PA2_dup2004"  "L1HS_dup811"    "L1PA2_dup2729"  "L1HS_dup370"   
## [429] "L1PA3_dup7840"  "L1PA2_dup4454"  "L1PA3_dup10531" "L1PA3_dup3950" 
## [433] "L1PA3_dup1027"  "L1PA2_dup3003"  "L1PA2_dup4226"  "L1PA3_dup247"  
## [437] "L1PA2_dup2876"  "L1PA3_dup6871"  "L1PA3_dup7316"  "L1PA3_dup4596" 
## [441] "L1PA2_dup3503"  "L1HS_dup802"    "L1PA2_dup98"    "L1PA2_dup3426" 
## [445] "L1PA3_dup5886"  "L1HS_dup803"    "L1PA3_dup8520"  "L1HS_dup1284"  
## [449] "L1PA3_dup5057"  "L1PA3_dup3291"  "L1PA3_dup2755"  "L1PA3_dup8896" 
## [453] "L1PA3_dup6112"  "L1PA2_dup514"   "L1PA2_dup3160"  "L1PA2_dup1653" 
## [457] "L1PA2_dup4430"  "L1PA3_dup683"   "L1PA3_dup6730"  "L1HS_dup579"   
## [461] "L1HS_dup62"     "L1PA2_dup2089"  "L1PA3_dup5238"  "L1PA2_dup2504" 
## [465] "L1PA3_dup6884"  "L1PA2_dup3930"  "L1PA2_dup3766"  "L1PA3_dup8117" 
## [469] "L1PA3_dup4408"  "L1PA3_dup1463"  "L1PA2_dup1463"  "L1PA2_dup684"  
## [473] "L1PA3_dup1046"  "L1PA2_dup2254"  "L1HS_dup1501"   "L1PA3_dup3484" 
## [477] "L1PA2_dup678"   "L1PA3_dup3729"  "L1PA2_dup4389"  "L1PA3_dup5510" 
## [481] "L1PA2_dup365"   "L1PA2_dup1112"  "L1PA3_dup2039"  "L1PA3_dup7288" 
## [485] "L1PA3_dup1114"  "L1PA3_dup2643"  "L1PA2_dup383"   "L1PA2_dup4367" 
## [489] "L1PA3_dup5927"  "L1PA2_dup1023"  "L1PA2_dup4043"  "L1PA3_dup6523" 
## [493] "L1PA2_dup2577"  "L1PA2_dup4612"  "L1PA2_dup1058"  "L1PA3_dup3880" 
## [497] "L1PA3_dup1026"  "L1PA3_dup7605"  "L1PA2_dup2261"  "L1HS_dup1514"  
## [501] "L1PA2_dup798"   "L1PA3_dup5363"  "L1HS_dup1616"   "L1PA3_dup840"  
## [505] "L1PA3_dup8313"  "L1PA3_dup1328"  "L1PA2_dup4611"  "L1HS_dup622"   
## [509] "L1HS_dup1295"   "L1PA2_dup307"   "L1PA2_dup1992"  "L1PA2_dup1248" 
## [513] "L1PA3_dup1337"  "L1PA2_dup4432"  "L1PA2_dup4713"  "L1PA3_dup4393" 
## [517] "L1PA3_dup5825"  "L1PA3_dup6160"  "L1PA3_dup9722"  "L1PA3_dup9866"

asap_heatmap_snRNA(region = c("PFC"), 
                   tes = data_TE_annotation[which(data_TE_annotation$type == "HERV"),"TE_id"], 
                   return_df = F, 
                   breaks = seq(0,15,length.out = 52), 
                   data = TE_data, 
                   group_cols = c("celltype"), 
                   index_row_reorder = c(HERVs_sorted_pfc),
                   order_cols_groups = order_cols_celltype,
                   title = "PFC HERV: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
                   annotation_cols = annotation_cols)

## $heatmap
## 
## $order_cols
##   [1] "AA_ASAP116_PD_NP22-55_PFC_0"      "ASAP155_ctrl_NP23-21_PFC_0"      
##   [3] "AA_ASAP151_PD_NP17-232_PFC_0"     "AA_ASAP90_ctrl_NP16-293_PFC_0"   
##   [5] "AA_ASAP89_ctrl_NP16-284_PFC_0"    "AA_ASAP153_ctrl_NP19-137_PFC_0"  
##   [7] "AA_ASAP83_NP16-119_ctrl_PFC_0"    "AA_ASAP152_PD_NP19-91_PFC_0"     
##   [9] "MJ_ASAP14_ctrl_NP16-164_PFC_0"    "DA480_ASAP15_ctrl_NP16-21_PFC_0" 
##  [11] "AA_ASAP86_NP18-148_ctrl_PFC_0"    "AA_ASAP80_PD_NP21-57_PFC_0"      
##  [13] "DA777_ASAP28_PD_NP17-191_PFC_0"   "DA809_ASAP30_PD_NP18-117_PFC_0"  
##  [15] "DA430_ASAP9_PD_NP16-162_PFC_0"    "AA_ASAP82_PD_NP21-217_PFC_0"     
##  [17] "DA509_ASAP36_PD_NP19-16_PFC_0"    "DA490_ASAP11_PD_P73_PFC_0"       
##  [19] "DA810_ASAP34_PD_NP18-304_PFC_0"   "DA428_ASAP13_ctrl_NP16-161_PFC_0"
##  [21] "DA488_ASAP16_ctrl_PT231_PFC_0"    "DA499_ASAP44_PD_NP19-255_PFC_0"  
##  [23] "DA432_ASAP12_PD_P74_PFC_0"        "DA806_ASAP58_ctrl_NP19-45_PFC_0" 
##  [25] "DA476_ASAP10_PD_NP16-25_PFC_0"    "DA795_ASAP55_ctrl_NP19-37_PFC_0" 
##  [27] "AA_ASAP145_ctrl_NP19-218_PFC_0"   "AA_ASAP85_NP18-46_ctrl_PFC_0"    
##  [29] "AA_ASAP91_ctrl_NP17-20_PFC_0"     "AA_ASAP81_PD_NP21-208_PFC_0"     
##  [31] "DA775_ASAP22_PD_NP16-269_PFC_0"   "DA804_ASAP49_ctrl_NP18-159_PFC_0"
##  [33] "DA813_ASAP17_PD_NP16-140_PFC_0"   "DA480_ASAP15_ctrl_NP16-21_PFC_1" 
##  [35] "AA_ASAP85_NP18-46_ctrl_PFC_1"     "DA795_ASAP55_ctrl_NP19-37_PFC_1" 
##  [37] "AA_ASAP153_ctrl_NP19-137_PFC_1"   "AA_ASAP91_ctrl_NP17-20_PFC_1"    
##  [39] "ASAP155_ctrl_NP23-21_PFC_1"       "AA_ASAP90_ctrl_NP16-293_PFC_1"   
##  [41] "AA_ASAP89_ctrl_NP16-284_PFC_1"    "MJ_ASAP14_ctrl_NP16-164_PFC_1"   
##  [43] "AA_ASAP116_PD_NP22-55_PFC_1"      "AA_ASAP151_PD_NP17-232_PFC_1"    
##  [45] "AA_ASAP145_ctrl_NP19-218_PFC_1"   "DA476_ASAP10_PD_NP16-25_PFC_1"   
##  [47] "DA777_ASAP28_PD_NP17-191_PFC_1"   "DA430_ASAP9_PD_NP16-162_PFC_1"   
##  [49] "AA_ASAP83_NP16-119_ctrl_PFC_1"    "DA809_ASAP30_PD_NP18-117_PFC_1"  
##  [51] "DA490_ASAP11_PD_P73_PFC_1"        "AA_ASAP82_PD_NP21-217_PFC_1"     
##  [53] "DA509_ASAP36_PD_NP19-16_PFC_1"    "AA_ASAP81_PD_NP21-208_PFC_1"     
##  [55] "AA_ASAP86_NP18-148_ctrl_PFC_1"    "AA_ASAP80_PD_NP21-57_PFC_1"      
##  [57] "DA499_ASAP44_PD_NP19-255_PFC_1"   "DA432_ASAP12_PD_P74_PFC_1"       
##  [59] "AA_ASAP152_PD_NP19-91_PFC_1"      "DA428_ASAP13_ctrl_NP16-161_PFC_1"
##  [61] "DA806_ASAP58_ctrl_NP19-45_PFC_1"  "DA810_ASAP34_PD_NP18-304_PFC_1"  
##  [63] "DA488_ASAP16_ctrl_PT231_PFC_1"    "DA775_ASAP22_PD_NP16-269_PFC_1"  
##  [65] "DA804_ASAP49_ctrl_NP18-159_PFC_1" "AA_ASAP82_PD_NP21-217_PFC_2"     
##  [67] "AA_ASAP90_ctrl_NP16-293_PFC_2"    "AA_ASAP152_PD_NP19-91_PFC_2"     
##  [69] "DA428_ASAP13_ctrl_NP16-161_PFC_2" "DA499_ASAP44_PD_NP19-255_PFC_2"  
##  [71] "DA810_ASAP34_PD_NP18-304_PFC_2"   "DA806_ASAP58_ctrl_NP19-45_PFC_2" 
##  [73] "DA488_ASAP16_ctrl_PT231_PFC_2"    "AA_ASAP86_NP18-148_ctrl_PFC_2"   
##  [75] "DA480_ASAP15_ctrl_NP16-21_PFC_2"  "AA_ASAP145_ctrl_NP19-218_PFC_2"  
##  [77] "DA476_ASAP10_PD_NP16-25_PFC_2"    "MJ_ASAP14_ctrl_NP16-164_PFC_2"   
##  [79] "DA430_ASAP9_PD_NP16-162_PFC_2"    "ASAP155_ctrl_NP23-21_PFC_2"      
##  [81] "AA_ASAP116_PD_NP22-55_PFC_2"      "AA_ASAP80_PD_NP21-57_PFC_2"      
##  [83] "AA_ASAP83_NP16-119_ctrl_PFC_2"    "AA_ASAP89_ctrl_NP16-284_PFC_2"   
##  [85] "DA795_ASAP55_ctrl_NP19-37_PFC_2"  "DA432_ASAP12_PD_P74_PFC_2"       
##  [87] "DA509_ASAP36_PD_NP19-16_PFC_2"    "DA490_ASAP11_PD_P73_PFC_2"       
##  [89] "AA_ASAP81_PD_NP21-208_PFC_2"      "AA_ASAP154_ctrl_NP21-04_PFC_2"   
##  [91] "AA_ASAP153_ctrl_NP19-137_PFC_2"   "AA_ASAP91_ctrl_NP17-20_PFC_2"    
##  [93] "AA_ASAP84_NP17-216_ctrl_PFC_2"    "DA785_ASAP47_ctrl_NP17-256_PFC_2"
##  [95] "AA_ASAP150_PD_NP16-285_PFC_2"     "DA809_ASAP30_PD_NP18-117_PFC_2"  
##  [97] "AA_ASAP151_PD_NP17-232_PFC_2"     "DA804_ASAP49_ctrl_NP18-159_PFC_2"
##  [99] "DA775_ASAP22_PD_NP16-269_PFC_2"   "DA808_ASAP41_PD_NP19-108_PFC_2"  
## [101] "DA490_ASAP11_PD_P73_PFC_3"        "DA509_ASAP36_PD_NP19-16_PFC_3"   
## [103] "AA_ASAP90_ctrl_NP16-293_PFC_3"    "AA_ASAP154_ctrl_NP21-04_PFC_3"   
## [105] "AA_ASAP86_NP18-148_ctrl_PFC_3"    "AA_ASAP152_PD_NP19-91_PFC_3"     
## [107] "ASAP155_ctrl_NP23-21_PFC_3"       "DA480_ASAP15_ctrl_NP16-21_PFC_3" 
## [109] "AA_ASAP116_PD_NP22-55_PFC_3"      "DA785_ASAP47_ctrl_NP17-256_PFC_3"
## [111] "MJ_ASAP14_ctrl_NP16-164_PFC_3"    "AA_ASAP151_PD_NP17-232_PFC_3"    
## [113] "AA_ASAP89_ctrl_NP16-284_PFC_3"    "AA_ASAP83_NP16-119_ctrl_PFC_3"   
## [115] "AA_ASAP82_PD_NP21-217_PFC_3"      "DA499_ASAP44_PD_NP19-255_PFC_3"  
## [117] "AA_ASAP80_PD_NP21-57_PFC_3"       "DA777_ASAP28_PD_NP17-191_PFC_3"  
## [119] "DA806_ASAP58_ctrl_NP19-45_PFC_3"  "DA810_ASAP34_PD_NP18-304_PFC_3"  
## [121] "DA488_ASAP16_ctrl_PT231_PFC_3"    "DA428_ASAP13_ctrl_NP16-161_PFC_3"
## [123] "DA430_ASAP9_PD_NP16-162_PFC_3"    "DA809_ASAP30_PD_NP18-117_PFC_3"  
## [125] "DA804_ASAP49_ctrl_NP18-159_PFC_3" "DA476_ASAP10_PD_NP16-25_PFC_3"   
## [127] "DA795_ASAP55_ctrl_NP19-37_PFC_3"  "DA775_ASAP22_PD_NP16-269_PFC_3"  
## [129] "AA_ASAP91_ctrl_NP17-20_PFC_3"     "AA_ASAP84_NP17-216_ctrl_PFC_3"   
## [131] "DA432_ASAP12_PD_P74_PFC_3"        "AA_ASAP150_PD_NP16-285_PFC_3"    
## [133] "AA_ASAP145_ctrl_NP19-218_PFC_3"   "AA_ASAP147_ctrl_NP22-37_PFC_5"   
## [135] "DA480_ASAP15_ctrl_NP16-21_PFC_5"  "AA_ASAP89_ctrl_NP16-284_PFC_5"   
## [137] "AA_ASAP90_ctrl_NP16-293_PFC_5"    "AA_ASAP85_NP18-46_ctrl_PFC_5"    
## [139] "DA490_ASAP11_PD_P73_PFC_5"        "DA509_ASAP36_PD_NP19-16_PFC_5"   
## [141] "DA430_ASAP9_PD_NP16-162_PFC_5"    "AA_ASAP91_ctrl_NP17-20_PFC_5"    
## [143] "AA_ASAP83_NP16-119_ctrl_PFC_5"    "DA775_ASAP22_PD_NP16-269_PFC_5"  
## [145] "DA806_ASAP58_ctrl_NP19-45_PFC_5"  "DA428_ASAP13_ctrl_NP16-161_PFC_5"
## [147] "DA777_ASAP28_PD_NP17-191_PFC_5"   "DA499_ASAP44_PD_NP19-255_PFC_5"  
## [149] "DA810_ASAP34_PD_NP18-304_PFC_5"   "DA488_ASAP16_ctrl_PT231_PFC_5"   
## [151] "AA_ASAP82_PD_NP21-217_PFC_5"      "AA_ASAP80_PD_NP21-57_PFC_5"      
## [153] "AA_ASAP86_NP18-148_ctrl_PFC_5"    "AA_ASAP152_PD_NP19-91_PFC_5"     
## [155] "ASAP155_ctrl_NP23-21_PFC_5"       "MJ_ASAP14_ctrl_NP16-164_PFC_5"   
## [157] "DA785_ASAP47_ctrl_NP17-256_PFC_5" "AA_ASAP84_NP17-216_ctrl_PFC_5"   
## [159] "AA_ASAP154_ctrl_NP21-04_PFC_5"    "DA799_ASAP19_PD_NP16-160_PFC_5"  
## [161] "DA432_ASAP12_PD_P74_PFC_5"        "AA_ASAP153_ctrl_NP19-137_PFC_5"  
## [163] "DA813_ASAP17_PD_NP16-140_PFC_5"   "AA_ASAP116_PD_NP22-55_PFC_5"     
## [165] "DA808_ASAP41_PD_NP19-108_PFC_5"   "AA_ASAP150_PD_NP16-285_PFC_5"    
## [167] "AA_ASAP151_PD_NP17-232_PFC_5"     "DA804_ASAP49_ctrl_NP18-159_PFC_5"
## [169] "DA476_ASAP10_PD_NP16-25_PFC_5"    "DA795_ASAP55_ctrl_NP19-37_PFC_5" 
## [171] "AA_ASAP145_ctrl_NP19-218_PFC_5"   "DA809_ASAP30_PD_NP18-117_PFC_5"  
## [173] "DA430_ASAP9_PD_NP16-162_PFC_4"    "AA_ASAP89_ctrl_NP16-284_PFC_4"   
## [175] "DA428_ASAP13_ctrl_NP16-161_PFC_4" "AA_ASAP152_PD_NP19-91_PFC_4"     
## [177] "AA_ASAP151_PD_NP17-232_PFC_4"     "DA806_ASAP58_ctrl_NP19-45_PFC_4" 
## [179] "AA_ASAP83_NP16-119_ctrl_PFC_4"    "DA488_ASAP16_ctrl_PT231_PFC_4"   
## [181] "AA_ASAP80_PD_NP21-57_PFC_4"       "DA480_ASAP15_ctrl_NP16-21_PFC_4" 
## [183] "ASAP155_ctrl_NP23-21_PFC_4"       "AA_ASAP145_ctrl_NP19-218_PFC_4"  
## [185] "MJ_ASAP14_ctrl_NP16-164_PFC_4"    "AA_ASAP90_ctrl_NP16-293_PFC_4"   
## [187] "DA499_ASAP44_PD_NP19-255_PFC_4"   "AA_ASAP82_PD_NP21-217_PFC_4"     
## [189] "DA775_ASAP22_PD_NP16-269_PFC_4"   "AA_ASAP86_NP18-148_ctrl_PFC_4"   
## [191] "DA432_ASAP12_PD_P74_PFC_4"        "DA490_ASAP11_PD_P73_PFC_4"       
## [193] "DA808_ASAP41_PD_NP19-108_PFC_4"   "DA804_ASAP49_ctrl_NP18-159_PFC_4"
## [195] "DA795_ASAP55_ctrl_NP19-37_PFC_4"  "AA_ASAP116_PD_NP22-55_PFC_4"     
## [197] "DA476_ASAP10_PD_NP16-25_PFC_4"    "DA785_ASAP47_ctrl_NP17-256_PFC_6"
## [199] "MJ_ASAP14_ctrl_NP16-164_PFC_6"    "AA_ASAP152_PD_NP19-91_PFC_6"     
## [201] "AA_ASAP89_ctrl_NP16-284_PFC_6"    "DA428_ASAP13_ctrl_NP16-161_PFC_6"
## 
## $order_rows
##   [1] "HERV_dup773"  "HERV_dup1758" "HERV_dup631"  "HERV_dup288"  "HERV_dup3252"
##   [6] "HERV_dup152"  "HERV_dup2491" "HERV_dup3390" "HERV_dup1281" "HERV_dup2856"
##  [11] "HERV_dup1708" "HERV_dup600"  "HERV_dup1209" "HERV_dup1"    "HERV_dup1079"
##  [16] "HERV_dup302"  "HERV_dup2841" "HERV_dup2966" "HERV_dup2838" "HERV_dup265" 
##  [21] "HERV_dup1050" "HERV_dup2880" "HERV_dup3357" "HERV_dup1702" "HERV_dup2273"
##  [26] "HERV_dup1000" "HERV_dup614"  "HERV_dup470"  "HERV_dup1283" "HERV_dup940" 
##  [31] "HERV_dup799"  "HERV_dup3226" "HERV_dup54"   "HERV_dup1888" "HERV_dup2900"
##  [36] "HERV_dup384"  "HERV_dup1339" "HERV_dup1669" "HERV_dup2381" "HERV_dup1357"
##  [41] "HERV_dup1102" "HERV_dup209"  "HERV_dup2789" "HERV_dup926"  "HERV_dup3171"
##  [46] "HERV_dup379"  "HERV_dup1456" "HERV_dup3174" "HERV_dup417"  "HERV_dup2365"
##  [51] "HERV_dup2182" "HERV_dup1004" "HERV_dup112"  "HERV_dup916"  "HERV_dup717" 
##  [56] "HERV_dup1356" "HERV_dup3105" "HERV_dup980"  "HERV_dup1308" "HERV_dup3423"
##  [61] "HERV_dup1243" "HERV_dup3379" "HERV_dup93"   "HERV_dup37"   "HERV_dup2012"
##  [66] "HERV_dup1701" "HERV_dup3355" "HERV_dup3248" "HERV_dup3363" "HERV_dup3673"
##  [71] "HERV_dup3266" "HERV_dup1319" "HERV_dup474"  "HERV_dup1203" "HERV_dup2106"
##  [76] "HERV_dup1208" "HERV_dup2376" "HERV_dup1309" "HERV_dup1272" "HERV_dup1657"
##  [81] "HERV_dup1362" "HERV_dup1002" "HERV_dup3375" "HERV_dup873"  "HERV_dup1310"
##  [86] "HERV_dup612"  "HERV_dup110"  "HERV_dup2529" "HERV_dup904"  "HERV_dup670" 
##  [91] "HERV_dup1598" "HERV_dup562"  "HERV_dup1255" "HERV_dup1327" "HERV_dup880" 
##  [96] "HERV_dup1663" "HERV_dup565"  "HERV_dup1038" "HERV_dup2292" "HERV_dup1724"
## [101] "HERV_dup518"  "HERV_dup2879" "HERV_dup682"  "HERV_dup1371" "HERV_dup831" 
## [106] "HERV_dup3343" "HERV_dup913"  "HERV_dup731"  "HERV_dup1382" "HERV_dup1670"
## [111] "HERV_dup1447" "HERV_dup151"  "HERV_dup1934" "HERV_dup2840" "HERV_dup1359"
## [116] "HERV_dup1048" "HERV_dup1307" "HERV_dup1449" "HERV_dup1749" "HERV_dup597" 
## [121] "HERV_dup2176" "HERV_dup2261" "HERV_dup1944" "HERV_dup739"  "HERV_dup2599"
## [126] "HERV_dup2217" "HERV_dup1334" "HERV_dup1315" "HERV_dup899"  "HERV_dup348" 
## [131] "HERV_dup57"   "HERV_dup293"  "HERV_dup1755" "HERV_dup1282" "HERV_dup355" 
## [136] "HERV_dup2894" "HERV_dup1001" "HERV_dup2902" "HERV_dup2550" "HERV_dup2137"
## [141] "HERV_dup1667" "HERV_dup1875" "HERV_dup969"  "HERV_dup1351" "HERV_dup2914"
## [146] "HERV_dup1694" "HERV_dup3107" "HERV_dup758"  "HERV_dup966"  "HERV_dup2299"
## [151] "HERV_dup1776" "HERV_dup26"   "HERV_dup2631" "HERV_dup3522" "HERV_dup1935"
## [156] "HERV_dup1345" "HERV_dup1611" "HERV_dup1052" "HERV_dup292"  "HERV_dup1512"
## [161] "HERV_dup2843" "HERV_dup613"  "HERV_dup2877" "HERV_dup1107" "HERV_dup3212"
## [166] "HERV_dup1269" "HERV_dup1081" "HERV_dup1932" "HERV_dup2530" "HERV_dup1364"
## [171] "HERV_dup1017" "HERV_dup2166" "HERV_dup301"  "HERV_dup5"    "HERV_dup3418"
## [176] "HERV_dup369"  "HERV_dup954"  "HERV_dup1007" "HERV_dup1940" "HERV_dup380" 
## [181] "HERV_dup1750" "HERV_dup2643" "HERV_dup1303" "HERV_dup1253" "HERV_dup65"  
## [186] "HERV_dup1232" "HERV_dup3196" "HERV_dup967"  "HERV_dup2566" "HERV_dup508" 
## [191] "HERV_dup2834" "HERV_dup876"  "HERV_dup1756" "HERV_dup1569" "HERV_dup1358"
## [196] "HERV_dup3270" "HERV_dup203"  "HERV_dup1302" "HERV_dup2589" "HERV_dup1416"
## [201] "HERV_dup872"  "HERV_dup2438" "HERV_dup3217" "HERV_dup2719" "HERV_dup487" 
## [206] "HERV_dup3033" "HERV_dup3417" "HERV_dup1613" "HERV_dup939"  "HERV_dup3140"
## [211] "HERV_dup2163" "HERV_dup482"  "HERV_dup2662" "HERV_dup1242" "HERV_dup2266"
## [216] "HERV_dup777"  "HERV_dup291"  "HERV_dup3580" "HERV_dup3050" "HERV_dup2250"
## [221] "HERV_dup3198" "HERV_dup1295" "HERV_dup2235" "HERV_dup2412" "HERV_dup471" 
## [226] "HERV_dup2939" "HERV_dup443"  "HERV_dup202"  "HERV_dup2188" "HERV_dup1484"
## [231] "HERV_dup1046" "HERV_dup290"  "HERV_dup1890" "HERV_dup215"  "HERV_dup3694"
## [236] "HERV_dup3529" "HERV_dup1617" "HERV_dup36"   "HERV_dup2736" "HERV_dup3231"
## [241] "HERV_dup2936" "HERV_dup1049" "HERV_dup1520" "HERV_dup34"   "HERV_dup399" 
## [246] "HERV_dup3251" "HERV_dup468"  "HERV_dup979"  "HERV_dup990"  "HERV_dup2803"
## [251] "HERV_dup2500" "HERV_dup2319" "HERV_dup3187" "HERV_dup433"  "HERV_dup1036"
## [256] "HERV_dup1605" "HERV_dup1707" "HERV_dup2752" "HERV_dup2857" "HERV_dup2963"
## [261] "HERV_dup2623" "HERV_dup282"  "HERV_dup2961" "HERV_dup2964" "HERV_dup3505"
## [266] "HERV_dup1662" "HERV_dup441"  "HERV_dup2735" "HERV_dup329"  "HERV_dup2905"
## [271] "HERV_dup890"  "HERV_dup949"  "HERV_dup1661" "HERV_dup2915" "HERV_dup586" 
## [276] "HERV_dup3124" "HERV_dup27"   "HERV_dup2978" "HERV_dup1917" "HERV_dup1596"
## [281] "HERV_dup249"  "HERV_dup2111" "HERV_dup870"  "HERV_dup1717" "HERV_dup94"  
## [286] "HERV_dup2093" "HERV_dup2588" "HERV_dup251"  "HERV_dup2464" "HERV_dup1112"
## [291] "HERV_dup1073" "HERV_dup18"   "HERV_dup3286" "HERV_dup1240" "HERV_dup3341"
## [296] "HERV_dup1658" "HERV_dup2179" "HERV_dup1331" "HERV_dup118"  "HERV_dup3358"
## [301] "HERV_dup505"  "HERV_dup3143" "HERV_dup2769" "HERV_dup2801" "HERV_dup2784"
## [306] "HERV_dup2264" "HERV_dup1846" "HERV_dup2603" "HERV_dup1437" "HERV_dup2353"
## [311] "HERV_dup1780" "HERV_dup377"  "HERV_dup1298" "HERV_dup1324" "HERV_dup1972"
## [316] "HERV_dup2847" "HERV_dup968"  "HERV_dup2129" "HERV_dup956"  "HERV_dup3118"
## [321] "HERV_dup2646" "HERV_dup2476" "HERV_dup1317" "HERV_dup1851" "HERV_dup492" 
## [326] "HERV_dup1316" "HERV_dup1703" "HERV_dup1236" "HERV_dup2812" "HERV_dup2878"
## [331] "HERV_dup2733" "HERV_dup2415" "HERV_dup2533" "HERV_dup58"   "HERV_dup2480"
## [336] "HERV_dup1321" "HERV_dup250"  "HERV_dup2855" "HERV_dup3406" "HERV_dup2130"
## [341] "HERV_dup1374" "HERV_dup724"  "HERV_dup2149" "HERV_dup23"   "HERV_dup2562"
## [346] "HERV_dup2607" "HERV_dup1089" "HERV_dup1187" "HERV_dup2298" "HERV_dup3020"
## [351] "HERV_dup2695" "HERV_dup1982" "HERV_dup469"  "HERV_dup1071" "HERV_dup1579"
## [356] "HERV_dup1401" "HERV_dup1268" "HERV_dup2337" "HERV_dup1673" "HERV_dup599" 
## [361] "HERV_dup1719" "HERV_dup3148" "HERV_dup2886" "HERV_dup1491" "HERV_dup1847"
## [366] "HERV_dup2747" "HERV_dup2941" "HERV_dup573"  "HERV_dup3459" "HERV_dup344" 
## [371] "HERV_dup661"  "HERV_dup2303" "HERV_dup3410" "HERV_dup1064" "HERV_dup1923"
## [376] "HERV_dup1720" "HERV_dup29"   "HERV_dup409"  "HERV_dup1322" "HERV_dup331" 
## [381] "HERV_dup1931" "HERV_dup1920" "HERV_dup2085" "HERV_dup1943" "HERV_dup2192"
## [386] "HERV_dup1210" "HERV_dup388"  "HERV_dup2282" "HERV_dup1731" "HERV_dup1389"
## [391] "HERV_dup1500" "HERV_dup1671" "HERV_dup2183" "HERV_dup2187" "HERV_dup1438"
## [396] "HERV_dup1005" "HERV_dup2598" "HERV_dup3342" "HERV_dup180"  "HERV_dup2730"
## [401] "HERV_dup1394" "HERV_dup3063" "HERV_dup1804" "HERV_dup1730" "HERV_dup2561"
## [406] "HERV_dup729"  "HERV_dup300"  "HERV_dup1350" "HERV_dup2907" "HERV_dup3365"
## [411] "HERV_dup467"  "HERV_dup850"  "HERV_dup386"  "HERV_dup2436" "HERV_dup214" 
## [416] "HERV_dup1201" "HERV_dup2809" "HERV_dup2383" "HERV_dup1973" "HERV_dup218" 
## [421] "HERV_dup1213" "HERV_dup2555" "HERV_dup3044" "HERV_dup2134" "HERV_dup2158"
## [426] "HERV_dup1629" "HERV_dup2949" "HERV_dup2518" "HERV_dup1556" "HERV_dup1218"
## [431] "HERV_dup1082" "HERV_dup665"  "HERV_dup3408" "HERV_dup1541" "HERV_dup3287"
## [436] "HERV_dup2848" "HERV_dup554"  "HERV_dup1823" "HERV_dup1802" "HERV_dup1638"
## [441] "HERV_dup1222" "HERV_dup1587" "HERV_dup1285" "HERV_dup2778" "HERV_dup3227"
## [446] "HERV_dup3117" "HERV_dup1378" "HERV_dup723"  "HERV_dup553"  "HERV_dup1297"
## [451] "HERV_dup3210" "HERV_dup1872" "HERV_dup2391" "HERV_dup2378" "HERV_dup1653"
## [456] "HERV_dup2891" "HERV_dup2112" "HERV_dup1090" "HERV_dup2962" "HERV_dup3430"
## [461] "HERV_dup3351" "HERV_dup1093" "HERV_dup1953" "HERV_dup2979" "HERV_dup632" 
## [466] "HERV_dup1914" "HERV_dup2967" "HERV_dup1668" "HERV_dup1513" "HERV_dup728" 
## [471] "HERV_dup1304" "HERV_dup243"  "HERV_dup1333" "HERV_dup2635" "HERV_dup272" 
## [476] "HERV_dup803"  "HERV_dup2366" "HERV_dup336"  "HERV_dup1757" "HERV_dup2379"
## [481] "HERV_dup1080" "HERV_dup1146" "HERV_dup3031" "HERV_dup2002" "HERV_dup626" 
## [486] "HERV_dup1273" "HERV_dup1453" "HERV_dup933"  "HERV_dup2604" "HERV_dup3507"
## [491] "HERV_dup2653" "HERV_dup662"  "HERV_dup115"  "HERV_dup2422" "HERV_dup2977"
## [496] "HERV_dup1889" "HERV_dup120"  "HERV_dup2242" "HERV_dup3388" "HERV_dup1156"
## [501] "HERV_dup852"  "HERV_dup2041" "HERV_dup1390" "HERV_dup1869" "HERV_dup1366"
## [506] "HERV_dup736"  "HERV_dup2706" "HERV_dup982"  "HERV_dup1933" "HERV_dup2278"
## [511] "HERV_dup2696" "HERV_dup314"  "HERV_dup2027" "HERV_dup935"  "HERV_dup556" 
## [516] "HERV_dup909"  "HERV_dup2524" "HERV_dup434"  "HERV_dup1412" "HERV_dup3008"
## [521] "HERV_dup3284" "HERV_dup356"  "HERV_dup3220" "HERV_dup882"  "HERV_dup509" 
## [526] "HERV_dup276"  "HERV_dup1948" "HERV_dup1103" "HERV_dup894"  "HERV_dup1891"
## [531] "HERV_dup3335" "HERV_dup1433" "HERV_dup108"  "HERV_dup2290" "HERV_dup2141"
## [536] "HERV_dup577"  "HERV_dup2934" "HERV_dup1245" "HERV_dup3108" "HERV_dup3179"
## [541] "HERV_dup1614" "HERV_dup2728" "HERV_dup1248" "HERV_dup2743" "HERV_dup3189"
## [546] "HERV_dup3215" "HERV_dup2548" "HERV_dup419"  "HERV_dup38"   "HERV_dup1108"
## [551] "HERV_dup1047" "HERV_dup703"  "HERV_dup1526" "HERV_dup1381" "HERV_dup1184"
## [556] "HERV_dup2823" "HERV_dup884"  "HERV_dup446"  "HERV_dup3100" "HERV_dup277" 
## [561] "HERV_dup2019" "HERV_dup1099" "HERV_dup746"  "HERV_dup3394" "HERV_dup1129"
## [566] "HERV_dup17"   "HERV_dup1029" "HERV_dup517"  "HERV_dup447"  "HERV_dup3319"
## [571] "HERV_dup1527" "HERV_dup2334" "HERV_dup2404" "HERV_dup851"  "HERV_dup977" 
## [576] "HERV_dup1114" "HERV_dup3182" "HERV_dup452"  "HERV_dup2536" "HERV_dup1639"
## [581] "HERV_dup1254" "HERV_dup1403" "HERV_dup3366" "HERV_dup450"  "HERV_dup321" 
## [586] "HERV_dup2985" "HERV_dup710"  "HERV_dup3181" "HERV_dup3416" "HERV_dup177" 
## [591] "HERV_dup3137" "HERV_dup1413" "HERV_dup551"  "HERV_dup1212" "HERV_dup2663"
## [596] "HERV_dup1926" "HERV_dup2272" "HERV_dup3688" "HERV_dup3328" "HERV_dup2804"
## [601] "HERV_dup776"  "HERV_dup2159" "HERV_dup846"  "HERV_dup3239" "HERV_dup2479"
## [606] "HERV_dup928"  "HERV_dup2896" "HERV_dup2945" "HERV_dup1549" "HERV_dup1962"
## [611] "HERV_dup2772" "HERV_dup732"  "HERV_dup1656" "HERV_dup2785" "HERV_dup519" 
## [616] "HERV_dup772"  "HERV_dup1383" "HERV_dup568"  "HERV_dup570"  "HERV_dup127" 
## [621] "HERV_dup3481" "HERV_dup3073" "HERV_dup2033" "HERV_dup488"  "HERV_dup185" 
## [626] "HERV_dup184"  "HERV_dup1979" "HERV_dup1417" "HERV_dup2797" "HERV_dup2152"
## [631] "HERV_dup1131" "HERV_dup39"   "HERV_dup1459" "HERV_dup1172" "HERV_dup2632"
## [636] "HERV_dup1470" "HERV_dup3606" "HERV_dup1278" "HERV_dup692"  "HERV_dup927" 
## [641] "HERV_dup1235" "HERV_dup1557" "HERV_dup2356" "HERV_dup900"  "HERV_dup578" 
## [646] "HERV_dup2942" "HERV_dup2937" "HERV_dup2441" "HERV_dup1640" "HERV_dup407" 
## [651] "HERV_dup61"   "HERV_dup400"  "HERV_dup640"  "HERV_dup671"  "HERV_dup3519"
## [656] "HERV_dup1182" "HERV_dup3131" "HERV_dup2739" "HERV_dup1239" "HERV_dup975" 
## [661] "HERV_dup2482" "HERV_dup1494" "HERV_dup2651" "HERV_dup1013" "HERV_dup461" 
## [666] "HERV_dup86"   "HERV_dup1937" "HERV_dup595"  "HERV_dup934"  "HERV_dup530" 
## [671] "HERV_dup2557" "HERV_dup2320" "HERV_dup194"  "HERV_dup1496" "HERV_dup133" 
## [676] "HERV_dup357"  "HERV_dup3219" "HERV_dup2647" "HERV_dup1195" "HERV_dup2128"
## [681] "HERV_dup1733" "HERV_dup981"  "HERV_dup350"  "HERV_dup129"  "HERV_dup572" 
## [686] "HERV_dup389"  "HERV_dup2034" "HERV_dup1655" "HERV_dup2100" "HERV_dup21"  
## [691] "HERV_dup3588" "HERV_dup173"  "HERV_dup1868" "HERV_dup1958" "HERV_dup1003"
## [696] "HERV_dup634"  "HERV_dup930"  "HERV_dup1014" "HERV_dup1346" "HERV_dup1514"
## [701] "HERV_dup201"  "HERV_dup1532" "HERV_dup591"  "HERV_dup2481" "HERV_dup1664"
## [706] "HERV_dup183"  "HERV_dup2620" "HERV_dup1440" "HERV_dup3013" "HERV_dup2680"
## [711] "HERV_dup2655" "HERV_dup3607" "HERV_dup1555" "HERV_dup1279" "HERV_dup1384"
## [716] "HERV_dup3015" "HERV_dup2897" "HERV_dup1228" "HERV_dup2525" "HERV_dup2972"
## [721] "HERV_dup1415" "HERV_dup1711" "HERV_dup1778" "HERV_dup1902" "HERV_dup398" 
## [726] "HERV_dup735"  "HERV_dup3154" "HERV_dup3545" "HERV_dup2324" "HERV_dup84"  
## [731] "HERV_dup2602" "HERV_dup381"  "HERV_dup1752" "HERV_dup2875" "HERV_dup3037"
## [736] "HERV_dup240"  "HERV_dup3016" "HERV_dup78"   "HERV_dup924"

asap_heatmap_snRNA(region = c("PUT"), 
                   tes = data_TE_annotation[which(data_TE_annotation$type == "HERV"),"TE_id"], 
                   return_df = F, 
                   breaks = seq(0,15,length.out = 52), 
                   data = TE_data, 
                   group_cols = c("celltype"), 
                   index_row_reorder = c(HERVs_sorted_put),
                   order_cols_groups = order_cols_celltype,
                   title = "PUT HERV: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
                   annotation_cols = annotation_cols)

## $heatmap
## 
## $order_cols
##   [1] "AA82_ASAP68_PD_NP18-117_PUT_0"   "AA71_ASAP70_PD_NP18-304_PUT_0"  
##   [3] "AA87_ASAP76_ctrl_NP18-159_PUT_0" "AA74_ASAP62_PD_NP16-140_PUT_0"  
##   [5] "AA_ASAP138_PD_NP16-285_PUT_0"    "AA_ASAP98_ctrl_NP16-119_PUT_0"  
##   [7] "AA_ASAP141_ctrl_NP19-218_PUT_0"  "AA_ASAP97_PD_NP21-57_PUT_0"     
##   [9] "AA79_ASAP64_PD_NP16-162_PUT_0"   "AA_ASAP100_ctrl_NP18-148_PUT_0" 
##  [11] "AA84_ASAP71_PD_NP19-16_PUT_0"    "AA_ASAP92_ctrl_NP16-284_PUT_1"  
##  [13] "AA_ASAP139_PD_NP17-232_PUT_1"    "AA79_ASAP64_PD_NP16-162_PUT_1"  
##  [15] "AA_ASAP144_PD_NP19-137_PUT_1"    "AA_ASAP100_ctrl_NP18-148_PUT_1" 
##  [17] "AA74_ASAP62_PD_NP16-140_PUT_1"   "AA87_ASAP76_ctrl_NP18-159_PUT_1"
##  [19] "AA_ASAP88_PD_NP21-217_PUT_1"     "AA71_ASAP70_PD_NP18-304_PUT_1"  
##  [21] "AA84_ASAP71_PD_NP19-16_PUT_1"    "AA_ASAP117_PD_NP22-55_PUT_1"    
##  [23] "AA_ASAP87_PD_NP21-208_PUT_1"     "AA83_ASAP69_PD_NP18-287_PUT_2"  
##  [25] "AA77_ASAP61_PD_NP16-25_PUT_2"    "AA_ASAP93_ctrl_NP16-293_PUT_2"  
##  [27] "AA86_ASAP73_PD_NP19-108_PUT_2"   "AA73_ASAP65_PD_NP16-269_PUT_2"  
##  [29] "AA81_ASAP67_PD_NP17-191_PUT_2"   "AA_ASAP96_ctrl_NP18-46_PUT_2"   
##  [31] "AA_ASAP141_ctrl_NP19-218_PUT_2"  "AA_ASAP140_PD_NP19-91_PUT_2"    
##  [33] "AA85_ASAP72_PD_NP19-23_PUT_2"    "AA_ASAP88_PD_NP21-217_PUT_2"    
##  [35] "AA82_ASAP68_PD_NP18-117_PUT_2"   "AA76_ASAP74_PD_NP19-255_PUT_2"  
##  [37] "AA71_ASAP70_PD_NP18-304_PUT_2"   "AA_ASAP87_PD_NP21-208_PUT_2"    
##  [39] "AA87_ASAP76_ctrl_NP18-159_PUT_2" "AA_ASAP100_ctrl_NP18-148_PUT_2" 
##  [41] "AA74_ASAP62_PD_NP16-140_PUT_2"   "AA84_ASAP71_PD_NP19-16_PUT_2"   
##  [43] "AA_ASAP97_PD_NP21-57_PUT_2"      "AA_ASAP138_PD_NP16-285_PUT_2"   
##  [45] "AA_ASAP144_PD_NP19-137_PUT_2"    "AA79_ASAP64_PD_NP16-162_PUT_2"  
##  [47] "AA_ASAP117_PD_NP22-55_PUT_2"     "AA_ASAP98_ctrl_NP16-119_PUT_2"  
##  [49] "AA_ASAP139_PD_NP17-232_PUT_2"    "AA_ASAP92_ctrl_NP16-284_PUT_2"  
##  [51] "AA88_ASAP77_ctrl_NP19-36_PUT_2"  "AA_ASAP94_ctrl_NP17-20_PUT_2"   
##  [53] "AA89_ASAP78_ctrl_NP19-37_PUT_2"  "AA_ASAP146_PD_NP21-04_PUT_2"    
##  [55] "AA_ASAP142_ctrl_NP22-37_PUT_3"   "AA74_ASAP62_PD_NP16-140_PUT_3"  
##  [57] "AA_ASAP138_PD_NP16-285_PUT_3"    "AA79_ASAP64_PD_NP16-162_PUT_3"  
##  [59] "AA_ASAP100_ctrl_NP18-148_PUT_3"  "AA_ASAP93_ctrl_NP16-293_PUT_3"  
##  [61] "AA_ASAP139_PD_NP17-232_PUT_3"    "AA89_ASAP78_ctrl_NP19-37_PUT_3" 
##  [63] "AA_ASAP149_PD_NP23-21_PUT_3"     "AA86_ASAP73_PD_NP19-108_PUT_3"  
##  [65] "AA76_ASAP74_PD_NP19-255_PUT_3"   "AA82_ASAP68_PD_NP18-117_PUT_3"  
##  [67] "AA_ASAP88_PD_NP21-217_PUT_3"     "AA88_ASAP77_ctrl_NP19-36_PUT_3" 
##  [69] "AA85_ASAP72_PD_NP19-23_PUT_3"    "AA83_ASAP69_PD_NP18-287_PUT_3"  
##  [71] "AA_ASAP87_PD_NP21-208_PUT_3"     "AA_ASAP117_PD_NP22-55_PUT_3"    
##  [73] "AA_ASAP98_ctrl_NP16-119_PUT_3"   "AA_ASAP96_ctrl_NP18-46_PUT_3"   
##  [75] "AA81_ASAP67_PD_NP17-191_PUT_3"   "AA73_ASAP65_PD_NP16-269_PUT_3"  
##  [77] "AA_ASAP140_PD_NP19-91_PUT_3"     "AA_ASAP141_ctrl_NP19-218_PUT_3" 
##  [79] "AA_ASAP144_PD_NP19-137_PUT_3"    "AA84_ASAP71_PD_NP19-16_PUT_3"   
##  [81] "AA_ASAP97_PD_NP21-57_PUT_3"      "AA87_ASAP76_ctrl_NP18-159_PUT_3"
##  [83] "AA_ASAP146_PD_NP21-04_PUT_3"     "AA71_ASAP70_PD_NP18-304_PUT_3"  
##  [85] "AA77_ASAP61_PD_NP16-25_PUT_3"    "AA_ASAP94_ctrl_NP17-20_PUT_3"   
##  [87] "AA_ASAP92_ctrl_NP16-284_PUT_3"   "AA_ASAP149_PD_NP23-21_PUT_5"    
##  [89] "AA78_ASAP63_PD_NP16-160_PUT_5"   "AA_ASAP92_ctrl_NP16-284_PUT_5"  
##  [91] "AA_ASAP146_PD_NP21-04_PUT_5"     "AA76_ASAP74_PD_NP19-255_PUT_5"  
##  [93] "AA82_ASAP68_PD_NP18-117_PUT_5"   "AA_ASAP93_ctrl_NP16-293_PUT_5"  
##  [95] "AA85_ASAP72_PD_NP19-23_PUT_5"    "AA_ASAP142_ctrl_NP22-37_PUT_5"  
##  [97] "AA73_ASAP65_PD_NP16-269_PUT_5"   "AA89_ASAP78_ctrl_NP19-37_PUT_5" 
##  [99] "AA_ASAP94_ctrl_NP17-20_PUT_5"    "AA86_ASAP73_PD_NP19-108_PUT_5"  
## [101] "AA_ASAP96_ctrl_NP18-46_PUT_5"    "AA_ASAP117_PD_NP22-55_PUT_5"    
## [103] "AA79_ASAP64_PD_NP16-162_PUT_5"   "AA71_ASAP70_PD_NP18-304_PUT_5"  
## [105] "AA_ASAP139_PD_NP17-232_PUT_5"    "AA_ASAP138_PD_NP16-285_PUT_5"   
## [107] "AA_ASAP141_ctrl_NP19-218_PUT_5"  "AA87_ASAP76_ctrl_NP18-159_PUT_5"
## [109] "AA_ASAP100_ctrl_NP18-148_PUT_5"  "AA_ASAP97_PD_NP21-57_PUT_5"     
## [111] "AA_ASAP87_PD_NP21-208_PUT_5"     "AA84_ASAP71_PD_NP19-16_PUT_5"   
## [113] "AA_ASAP88_PD_NP21-217_PUT_5"     "AA88_ASAP77_ctrl_NP19-36_PUT_5" 
## [115] "AA_ASAP98_ctrl_NP16-119_PUT_5"   "AA74_ASAP62_PD_NP16-140_PUT_5"  
## [117] "AA83_ASAP69_PD_NP18-287_PUT_5"   "AA81_ASAP67_PD_NP17-191_PUT_5"  
## [119] "AA77_ASAP61_PD_NP16-25_PUT_5"    "AA_ASAP144_PD_NP19-137_PUT_5"   
## [121] "AA_ASAP140_PD_NP19-91_PUT_5"     "AA73_ASAP65_PD_NP16-269_PUT_4"  
## [123] "AA_ASAP88_PD_NP21-217_PUT_4"     "AA_ASAP140_PD_NP19-91_PUT_4"    
## [125] "AA_ASAP96_ctrl_NP18-46_PUT_4"    "AA85_ASAP72_PD_NP19-23_PUT_4"   
## [127] "AA_ASAP87_PD_NP21-208_PUT_4"     "AA_ASAP98_ctrl_NP16-119_PUT_4"  
## [129] "AA_ASAP117_PD_NP22-55_PUT_4"     "AA89_ASAP78_ctrl_NP19-37_PUT_4" 
## [131] "AA_ASAP94_ctrl_NP17-20_PUT_4"    "AA_ASAP138_PD_NP16-285_PUT_4"   
## [133] "AA_ASAP141_ctrl_NP19-218_PUT_4"  "AA76_ASAP74_PD_NP19-255_PUT_4"  
## [135] "AA83_ASAP69_PD_NP18-287_PUT_4"   "AA71_ASAP70_PD_NP18-304_PUT_4"  
## [137] "AA84_ASAP71_PD_NP19-16_PUT_4"    "AA_ASAP144_PD_NP19-137_PUT_4"   
## [139] "AA79_ASAP64_PD_NP16-162_PUT_4"   "AA87_ASAP76_ctrl_NP18-159_PUT_4"
## [141] "AA_ASAP100_ctrl_NP18-148_PUT_4"  "AA_ASAP97_PD_NP21-57_PUT_4"     
## [143] "AA77_ASAP61_PD_NP16-25_PUT_4"    "AA81_ASAP67_PD_NP17-191_PUT_4"  
## [145] "AA74_ASAP62_PD_NP16-140_PUT_4"  
## 
## $order_rows
##   [1] "HERV_dup773"  "HERV_dup1758" "HERV_dup1708" "HERV_dup3252" "HERV_dup1"   
##   [6] "HERV_dup288"  "HERV_dup152"  "HERV_dup2491" "HERV_dup3390" "HERV_dup631" 
##  [11] "HERV_dup2856" "HERV_dup2841" "HERV_dup1079" "HERV_dup600"  "HERV_dup3357"
##  [16] "HERV_dup1209" "HERV_dup1050" "HERV_dup2966" "HERV_dup302"  "HERV_dup1000"
##  [21] "HERV_dup265"  "HERV_dup1702" "HERV_dup2838" "HERV_dup831"  "HERV_dup54"  
##  [26] "HERV_dup1281" "HERV_dup2880" "HERV_dup470"  "HERV_dup1283" "HERV_dup2900"
##  [31] "HERV_dup1456" "HERV_dup2381" "HERV_dup93"   "HERV_dup2273" "HERV_dup799" 
##  [36] "HERV_dup1669" "HERV_dup1888" "HERV_dup1102" "HERV_dup209"  "HERV_dup1357"
##  [41] "HERV_dup3266" "HERV_dup2789" "HERV_dup940"  "HERV_dup1339" "HERV_dup980" 
##  [46] "HERV_dup384"  "HERV_dup3226" "HERV_dup379"  "HERV_dup1309" "HERV_dup1356"
##  [51] "HERV_dup1308" "HERV_dup2365" "HERV_dup2550" "HERV_dup565"  "HERV_dup2376"
##  [56] "HERV_dup1598" "HERV_dup3423" "HERV_dup3174" "HERV_dup474"  "HERV_dup1203"
##  [61] "HERV_dup2879" "HERV_dup3105" "HERV_dup1657" "HERV_dup1701" "HERV_dup1004"
##  [66] "HERV_dup518"  "HERV_dup1002" "HERV_dup873"  "HERV_dup1362" "HERV_dup112" 
##  [71] "HERV_dup2182" "HERV_dup151"  "HERV_dup926"  "HERV_dup1243" "HERV_dup2012"
##  [76] "HERV_dup3363" "HERV_dup614"  "HERV_dup1310" "HERV_dup1048" "HERV_dup3375"
##  [81] "HERV_dup1670" "HERV_dup717"  "HERV_dup1272" "HERV_dup3379" "HERV_dup562" 
##  [86] "HERV_dup37"   "HERV_dup1052" "HERV_dup1449" "HERV_dup1319" "HERV_dup2106"
##  [91] "HERV_dup731"  "HERV_dup3343" "HERV_dup2941" "HERV_dup369"  "HERV_dup880" 
##  [96] "HERV_dup3171" "HERV_dup1036" "HERV_dup1447" "HERV_dup1208" "HERV_dup1663"
## [101] "HERV_dup612"  "HERV_dup597"  "HERV_dup966"  "HERV_dup417"  "HERV_dup1315"
## [106] "HERV_dup904"  "HERV_dup1371" "HERV_dup1359" "HERV_dup1255" "HERV_dup2176"
## [111] "HERV_dup292"  "HERV_dup1667" "HERV_dup2530" "HERV_dup2599" "HERV_dup3355"
## [116] "HERV_dup380"  "HERV_dup3196" "HERV_dup1382" "HERV_dup1334" "HERV_dup57"  
## [121] "HERV_dup979"  "HERV_dup2292" "HERV_dup3107" "HERV_dup1232" "HERV_dup2631"
## [126] "HERV_dup2843" "HERV_dup1351" "HERV_dup2847" "HERV_dup2589" "HERV_dup2914"
## [131] "HERV_dup301"  "HERV_dup293"  "HERV_dup1282" "HERV_dup758"  "HERV_dup2261"
## [136] "HERV_dup1512" "HERV_dup3522" "HERV_dup1273" "HERV_dup899"  "HERV_dup1755"
## [141] "HERV_dup2217" "HERV_dup1345" "HERV_dup1750" "HERV_dup954"  "HERV_dup913" 
## [146] "HERV_dup1940" "HERV_dup348"  "HERV_dup1776" "HERV_dup3529" "HERV_dup1596"
## [151] "HERV_dup1001" "HERV_dup1749" "HERV_dup3140" "HERV_dup2438" "HERV_dup1934"
## [156] "HERV_dup2784" "HERV_dup2785" "HERV_dup3694" "HERV_dup1661" "HERV_dup1384"
## [161] "HERV_dup916"  "HERV_dup5"    "HERV_dup26"   "HERV_dup1081" "HERV_dup1107"
## [166] "HERV_dup2752" "HERV_dup1269" "HERV_dup2964" "HERV_dup1694" "HERV_dup1303"
## [171] "HERV_dup1846" "HERV_dup939"  "HERV_dup2963" "HERV_dup1112" "HERV_dup670" 
## [176] "HERV_dup2250" "HERV_dup3050" "HERV_dup3580" "HERV_dup2422" "HERV_dup949" 
## [181] "HERV_dup3418" "HERV_dup2111" "HERV_dup1007" "HERV_dup409"  "HERV_dup355" 
## [186] "HERV_dup2235" "HERV_dup110"  "HERV_dup3417" "HERV_dup1307" "HERV_dup1875"
## [191] "HERV_dup2166" "HERV_dup2299" "HERV_dup1358" "HERV_dup3358" "HERV_dup2353"
## [196] "HERV_dup2266" "HERV_dup2412" "HERV_dup1780" "HERV_dup1847" "HERV_dup2643"
## [201] "HERV_dup3505" "HERV_dup3198" "HERV_dup2840" "HERV_dup2662" "HERV_dup468" 
## [206] "HERV_dup487"  "HERV_dup36"   "HERV_dup482"  "HERV_dup2603" "HERV_dup1611"
## [211] "HERV_dup1071" "HERV_dup2961" "HERV_dup2034" "HERV_dup969"  "HERV_dup94"  
## [216] "HERV_dup2801" "HERV_dup1662" "HERV_dup1920" "HERV_dup3033" "HERV_dup1046"
## [221] "HERV_dup2623" "HERV_dup2733" "HERV_dup203"  "HERV_dup990"  "HERV_dup118" 
## [226] "HERV_dup1569" "HERV_dup554"  "HERV_dup1613" "HERV_dup329"  "HERV_dup2481"
## [231] "HERV_dup956"  "HERV_dup133"  "HERV_dup2566" "HERV_dup3124" "HERV_dup3108"
## [236] "HERV_dup18"   "HERV_dup2803" "HERV_dup1756" "HERV_dup1717" "HERV_dup1703"
## [241] "HERV_dup872"  "HERV_dup29"   "HERV_dup58"   "HERV_dup930"  "HERV_dup1851"
## [246] "HERV_dup2646" "HERV_dup1184" "HERV_dup2719" "HERV_dup400"  "HERV_dup433" 
## [251] "HERV_dup1416" "HERV_dup586"  "HERV_dup3341" "HERV_dup202"  "HERV_dup1017"
## [256] "HERV_dup1316" "HERV_dup2482" "HERV_dup661"  "HERV_dup2604" "HERV_dup2383"
## [261] "HERV_dup86"   "HERV_dup2743" "HERV_dup968"  "HERV_dup2163" "HERV_dup290" 
## [266] "HERV_dup1707" "HERV_dup1240" "HERV_dup240"  "HERV_dup471"  "HERV_dup65"  
## [271] "HERV_dup1253" "HERV_dup282"  "HERV_dup1653" "HERV_dup1935" "HERV_dup2192"
## [276] "HERV_dup2834" "HERV_dup682"  "HERV_dup2877" "HERV_dup732"  "HERV_dup573" 
## [281] "HERV_dup34"   "HERV_dup1236" "HERV_dup2112" "HERV_dup1932" "HERV_dup3406"
## [286] "HERV_dup2158" "HERV_dup2905" "HERV_dup1302" "HERV_dup2588" "HERV_dup2857"
## [291] "HERV_dup2939" "HERV_dup2937" "HERV_dup2085" "HERV_dup1931" "HERV_dup2264"
## [296] "HERV_dup1317" "HERV_dup3020" "HERV_dup214"  "HERV_dup2769" "HERV_dup3270"
## [301] "HERV_dup3519" "HERV_dup249"  "HERV_dup300"  "HERV_dup1374" "HERV_dup1605"
## [306] "HERV_dup2476" "HERV_dup398"  "HERV_dup2736" "HERV_dup1089" "HERV_dup356" 
## [311] "HERV_dup3251" "HERV_dup243"  "HERV_dup1389" "HERV_dup3187" "HERV_dup1484"
## [316] "HERV_dup1187" "HERV_dup1982" "HERV_dup2093" "HERV_dup2878" "HERV_dup613" 
## [321] "HERV_dup1730" "HERV_dup1541" "HERV_dup2500" "HERV_dup1752" "HERV_dup108" 
## [326] "HERV_dup321"  "HERV_dup3365" "HERV_dup3507" "HERV_dup2598" "HERV_dup1201"
## [331] "HERV_dup2902" "HERV_dup3148" "HERV_dup2524" "HERV_dup1890" "HERV_dup1195"
## [336] "HERV_dup1917" "HERV_dup2533" "HERV_dup218"  "HERV_dup388"  "HERV_dup1889"
## [341] "HERV_dup1304" "HERV_dup777"  "HERV_dup492"  "HERV_dup3063" "HERV_dup1973"
## [346] "HERV_dup1658" "HERV_dup2129" "HERV_dup1295" "HERV_dup1923" "HERV_dup1943"
## [351] "HERV_dup2562" "HERV_dup728"  "HERV_dup626"  "HERV_dup1324" "HERV_dup3545"
## [356] "HERV_dup2607" "HERV_dup890"  "HERV_dup1802" "HERV_dup1073" "HERV_dup1182"
## [361] "HERV_dup3388" "HERV_dup1156" "HERV_dup1438" "HERV_dup2778" "HERV_dup882" 
## [366] "HERV_dup3408" "HERV_dup2303" "HERV_dup180"  "HERV_dup1298" "HERV_dup1285"
## [371] "HERV_dup3410" "HERV_dup1108" "HERV_dup1242" "HERV_dup467"  "HERV_dup3210"
## [376] "HERV_dup3181" "HERV_dup2188" "HERV_dup1731" "HERV_dup1719" "HERV_dup2735"
## [381] "HERV_dup2942" "HERV_dup803"  "HERV_dup3430" "HERV_dup1331" "HERV_dup1557"
## [386] "HERV_dup1972" "HERV_dup1005" "HERV_dup344"  "HERV_dup1390" "HERV_dup3328"
## [391] "HERV_dup2187" "HERV_dup277"  "HERV_dup3342" "HERV_dup1394" "HERV_dup441" 
## [396] "HERV_dup2696" "HERV_dup2695" "HERV_dup1869" "HERV_dup1948" "HERV_dup272" 
## [401] "HERV_dup2480" "HERV_dup331"  "HERV_dup735"  "HERV_dup599"  "HERV_dup3227"
## [406] "HERV_dup1378" "HERV_dup1321" "HERV_dup3179" "HERV_dup2379" "HERV_dup1953"
## [411] "HERV_dup2936" "HERV_dup909"  "HERV_dup1278" "HERV_dup2962" "HERV_dup1268"
## [416] "HERV_dup2179" "HERV_dup1617" "HERV_dup2812" "HERV_dup1629" "HERV_dup1437"
## [421] "HERV_dup61"   "HERV_dup2891" "HERV_dup399"  "HERV_dup3143" "HERV_dup443" 
## [426] "HERV_dup215"  "HERV_dup3220" "HERV_dup2159" "HERV_dup1210" "HERV_dup1433"
## [431] "HERV_dup928"  "HERV_dup3351" "HERV_dup1453" "HERV_dup2561" "HERV_dup2739"
## [436] "HERV_dup2404" "HERV_dup3394" "HERV_dup3607" "HERV_dup27"   "HERV_dup2391"
## [441] "HERV_dup2949" "HERV_dup127"  "HERV_dup729"  "HERV_dup3287" "HERV_dup572" 
## [446] "HERV_dup723"  "HERV_dup2797" "HERV_dup1297" "HERV_dup78"   "HERV_dup2290"
## [451] "HERV_dup1333" "HERV_dup386"  "HERV_dup2324" "HERV_dup530"  "HERV_dup1440"
## [456] "HERV_dup2907" "HERV_dup2152" "HERV_dup1412" "HERV_dup1587" "HERV_dup1914"
## [461] "HERV_dup3286" "HERV_dup772"  "HERV_dup2635" "HERV_dup3013" "HERV_dup517" 
## [466] "HERV_dup1218" "HERV_dup736"  "HERV_dup2896" "HERV_dup3100" "HERV_dup2278"
## [471] "HERV_dup3688" "HERV_dup1254" "HERV_dup3137" "HERV_dup2663" "HERV_dup201" 
## [476] "HERV_dup1213" "HERV_dup3366" "HERV_dup3319" "HERV_dup2536" "HERV_dup2134"
## [481] "HERV_dup662"  "HERV_dup1222" "HERV_dup1500" "HERV_dup3217" "HERV_dup2967"
## [486] "HERV_dup1129" "HERV_dup377"  "HERV_dup1114" "HERV_dup894"  "HERV_dup3231"
## [491] "HERV_dup1350" "HERV_dup2141" "HERV_dup852"  "HERV_dup1640" "HERV_dup2320"
## [496] "HERV_dup2298" "HERV_dup2855" "HERV_dup2378" "HERV_dup1248" "HERV_dup3239"
## [501] "HERV_dup469"  "HERV_dup3606" "HERV_dup1029" "HERV_dup1804" "HERV_dup129" 
## [506] "HERV_dup2518" "HERV_dup2706" "HERV_dup2804" "HERV_dup1381" "HERV_dup21"  
## [511] "HERV_dup2183" "HERV_dup1579" "HERV_dup876"  "HERV_dup2897" "HERV_dup2130"
## [516] "HERV_dup1366" "HERV_dup2282" "HERV_dup870"  "HERV_dup2041" "HERV_dup1090"
## [521] "HERV_dup1279" "HERV_dup1470" "HERV_dup184"  "HERV_dup2033" "HERV_dup1757"
## [526] "HERV_dup2356" "HERV_dup553"  "HERV_dup927"  "HERV_dup2647" "HERV_dup1526"
## [531] "HERV_dup1103" "HERV_dup1720" "HERV_dup900"  "HERV_dup2019" "HERV_dup851" 
## [536] "HERV_dup1556" "HERV_dup17"   "HERV_dup251"  "HERV_dup1082" "HERV_dup2436"
## [541] "HERV_dup2728" "HERV_dup933"  "HERV_dup2915" "HERV_dup419"  "HERV_dup3481"
## [546] "HERV_dup1671" "HERV_dup1080" "HERV_dup115"  "HERV_dup3118" "HERV_dup2886"
## [551] "HERV_dup3416" "HERV_dup632"  "HERV_dup1212" "HERV_dup1047" "HERV_dup3248"
## [556] "HERV_dup2934" "HERV_dup488"  "HERV_dup703"  "HERV_dup710"  "HERV_dup935" 
## [561] "HERV_dup1868" "HERV_dup3215" "HERV_dup3673" "HERV_dup924"  "HERV_dup2747"
## [566] "HERV_dup1724" "HERV_dup120"  "HERV_dup577"  "HERV_dup1979" "HERV_dup1413"
## [571] "HERV_dup934"  "HERV_dup407"  "HERV_dup1383" "HERV_dup2529" "HERV_dup568" 
## [576] "HERV_dup982"  "HERV_dup2002" "HERV_dup2848" "HERV_dup2100" "HERV_dup2557"
## [581] "HERV_dup357"  "HERV_dup2809" "HERV_dup23"   "HERV_dup3212" "HERV_dup2823"
## [586] "HERV_dup1891" "HERV_dup1235" "HERV_dup1014" "HERV_dup2548" "HERV_dup967" 
## [591] "HERV_dup1962" "HERV_dup1926" "HERV_dup846"  "HERV_dup434"  "HERV_dup519" 
## [596] "HERV_dup1093" "HERV_dup2977" "HERV_dup2149" "HERV_dup975"  "HERV_dup776" 
## [601] "HERV_dup38"   "HERV_dup3182" "HERV_dup665"  "HERV_dup1937" "HERV_dup1668"
## [606] "HERV_dup1532" "HERV_dup2655" "HERV_dup2651" "HERV_dup3459" "HERV_dup1944"
## [611] "HERV_dup692"  "HERV_dup1415" "HERV_dup1364" "HERV_dup1673" "HERV_dup2653"
## [616] "HERV_dup2319" "HERV_dup2555" "HERV_dup2945" "HERV_dup1064" "HERV_dup2334"
## [621] "HERV_dup3219" "HERV_dup2242" "HERV_dup1245" "HERV_dup2620" "HERV_dup2985"
## [626] "HERV_dup2979" "HERV_dup3131" "HERV_dup739"  "HERV_dup3008" "HERV_dup556" 
## [631] "HERV_dup1131" "HERV_dup591"  "HERV_dup3037" "HERV_dup2525" "HERV_dup1038"
## [636] "HERV_dup2366" "HERV_dup250"  "HERV_dup2027" "HERV_dup595"  "HERV_dup1614"
## [641] "HERV_dup2415" "HERV_dup1049" "HERV_dup1555" "HERV_dup314"  "HERV_dup1239"
## [646] "HERV_dup276"  "HERV_dup3588" "HERV_dup884"  "HERV_dup1228" "HERV_dup1403"
## [651] "HERV_dup194"  "HERV_dup1401" "HERV_dup1778" "HERV_dup1099" "HERV_dup1013"
## [656] "HERV_dup1902" "HERV_dup183"  "HERV_dup3117" "HERV_dup2632" "HERV_dup2272"
## [661] "HERV_dup1513" "HERV_dup634"  "HERV_dup2137" "HERV_dup2464" "HERV_dup173" 
## [666] "HERV_dup3189" "HERV_dup336"  "HERV_dup39"   "HERV_dup1655" "HERV_dup350" 
## [671] "HERV_dup3284" "HERV_dup2337" "HERV_dup177"  "HERV_dup2128" "HERV_dup291" 
## [676] "HERV_dup640"  "HERV_dup446"  "HERV_dup551"  "HERV_dup3031" "HERV_dup724" 
## [681] "HERV_dup850"  "HERV_dup1494" "HERV_dup1933" "HERV_dup1327" "HERV_dup185" 
## [686] "HERV_dup1639" "HERV_dup1496" "HERV_dup1322" "HERV_dup570"  "HERV_dup3044"
## [691] "HERV_dup2894" "HERV_dup746"  "HERV_dup1656" "HERV_dup981"  "HERV_dup1733"
## [696] "HERV_dup977"  "HERV_dup3073" "HERV_dup505"  "HERV_dup578"  "HERV_dup1872"
## [701] "HERV_dup447"  "HERV_dup1527" "HERV_dup1146" "HERV_dup389"  "HERV_dup508" 
## [706] "HERV_dup2978" "HERV_dup1549" "HERV_dup2441" "HERV_dup3335" "HERV_dup1664"
## [711] "HERV_dup2772" "HERV_dup1823" "HERV_dup2602" "HERV_dup461"  "HERV_dup450" 
## [716] "HERV_dup671"  "HERV_dup1958" "HERV_dup509"  "HERV_dup1491" "HERV_dup3015"
## [721] "HERV_dup3154" "HERV_dup1520" "HERV_dup1346" "HERV_dup1638" "HERV_dup1172"
## [726] "HERV_dup1514" "HERV_dup2479" "HERV_dup452"  "HERV_dup2875" "HERV_dup2730"
## [731] "HERV_dup1459" "HERV_dup84"   "HERV_dup1711" "HERV_dup2680" "HERV_dup2972"
## [736] "HERV_dup1417" "HERV_dup381"  "HERV_dup1003" "HERV_dup3016"

asap_heatmap_snRNA(region = c("AMY"), 
                   tes = data_TE_annotation[which(data_TE_annotation$type == "HERV"),"TE_id"], 
                   return_df = F, 
                   breaks = seq(0,15,length.out = 52), 
                   data = TE_data, 
                   group_cols = c("celltype"), 
                   index_row_reorder = c(HERVs_sorted_amy),
                   order_cols_groups = order_cols_celltype,
                   title = "AMY HERV: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
                   annotation_cols = annotation_cols)

## $heatmap
## 
## $order_cols
##   [1] "AA_ASAP114_PD_NP21-57_AMY_0"      "DA811_ASAP18_PD_NP16-140_AMY_0"  
##   [3] "DA802_ASAP40_PD_NP19-23_AMY_0"    "DA780_ASAP37_PD_NP19-16_AMY_0"   
##   [5] "AA_ASAP110_ctrl_NP16-119_AMY_0"   "AA_ASAP115_PD_NP21-208_AMY_0"    
##   [7] "DA783_ASAP45_PD_NP19-255_AMY_0"   "DA474_ASAP24_PD_NP16-25_AMY_0"   
##   [9] "DA778_ASAP31_PD_NP18-117_AMY_0"   "DA791_ASAP50_ctrl_NP18-159_AMY_0"
##  [11] "DA793_ASAP53_ctrl_NP19-36_AMY_0"  "DA805_ASAP56_ctrl_NP19-37_AMY_0" 
##  [13] "AA_ASAP123_ctrl_NP19-218_AMY_1"   "AA_ASAP114_PD_NP21-57_AMY_1"     
##  [15] "AA_ASAP113_ctrl_NP18-148_AMY_1"   "AA_ASAP126_PD_NP19-137_AMY_1"    
##  [17] "AA_ASAP115_PD_NP21-208_AMY_1"     "AA_ASAP110_ctrl_NP16-119_AMY_1"  
##  [19] "DA512_ASAP60_ctrl_NP19-45_AMY_1"  "AA_ASAP124_ctrl_NP22-37_AMY_1"   
##  [21] "AA_ASAP119_PD_NP22-55_AMY_1"      "AA_ASAP121_PD_NP17-232_AMY_1"    
##  [23] "AA_ASAP128_PD_NP21-04_AMY_1"      "AA_ASAP131_PD_NP23-21_AMY_1"     
##  [25] "AA_ASAP109_PD_NP21-217_AMY_1"     "DA811_ASAP18_PD_NP16-140_AMY_1"  
##  [27] "DA793_ASAP53_ctrl_NP19-36_AMY_1"  "DA783_ASAP45_PD_NP19-255_AMY_1"  
##  [29] "DA474_ASAP24_PD_NP16-25_AMY_1"    "DA791_ASAP50_ctrl_NP18-159_AMY_1"
##  [31] "DA778_ASAP31_PD_NP18-117_AMY_1"   "DA805_ASAP56_ctrl_NP19-37_AMY_1" 
##  [33] "DA802_ASAP40_PD_NP19-23_AMY_1"    "DA801_ASAP53_ctrl_NP19-36_AMY_1" 
##  [35] "DA780_ASAP37_PD_NP19-16_AMY_1"    "ASAP122_PD_NP19-91_AMY_2"        
##  [37] "AA_ASAP128_PD_NP21-04_AMY_2"      "AA_ASAP120_PD_NP16-285_AMY_2"    
##  [39] "AA_ASAP119_PD_NP22-55_AMY_2"      "AA_ASAP109_PD_NP21-217_AMY_2"    
##  [41] "AA_ASAP126_PD_NP19-137_AMY_2"     "AA_ASAP131_PD_NP23-21_AMY_2"     
##  [43] "DA814_ASAP35_PD_NP18-304_AMY_2"   "DA801_ASAP53_ctrl_NP19-36_AMY_2" 
##  [45] "DA778_ASAP31_PD_NP18-117_AMY_2"   "DA793_ASAP53_ctrl_NP19-36_AMY_2" 
##  [47] "AA_ASAP110_ctrl_NP16-119_AMY_2"   "AA_ASAP114_PD_NP21-57_AMY_2"     
##  [49] "AA_ASAP123_ctrl_NP19-218_AMY_2"   "DA805_ASAP56_ctrl_NP19-37_AMY_2" 
##  [51] "AA_ASAP121_PD_NP17-232_AMY_2"     "DA811_ASAP18_PD_NP16-140_AMY_2"  
##  [53] "AA_ASAP112_ctrl_NP16-293_AMY_2"   "DA512_ASAP60_ctrl_NP19-45_AMY_2" 
##  [55] "AA_ASAP113_ctrl_NP18-148_AMY_2"   "DA807_ASAP29_PD_NP17-191_AMY_2"  
##  [57] "DA474_ASAP24_PD_NP16-25_AMY_2"    "AA_ASAP115_PD_NP21-208_AMY_2"    
##  [59] "DA783_ASAP45_PD_NP19-255_AMY_2"   "DA791_ASAP50_ctrl_NP18-159_AMY_2"
##  [61] "DA802_ASAP40_PD_NP19-23_AMY_2"    "AA_ASAP124_ctrl_NP22-37_AMY_2"   
##  [63] "DA780_ASAP37_PD_NP19-16_AMY_2"    "DA811_ASAP18_PD_NP16-140_AMY_3"  
##  [65] "AA_ASAP119_PD_NP22-55_AMY_3"      "AA_ASAP121_PD_NP17-232_AMY_3"    
##  [67] "AA_ASAP109_PD_NP21-217_AMY_3"     "DA802_ASAP40_PD_NP19-23_AMY_3"   
##  [69] "AA_ASAP111_ctrl_NP16-284_AMY_3"   "DA803_ASAP48_ctrl_NP17-256_AMY_3"
##  [71] "AA_ASAP120_PD_NP16-285_AMY_3"     "ASAP122_PD_NP19-91_AMY_3"        
##  [73] "AA_ASAP115_PD_NP21-208_AMY_3"     "DA783_ASAP45_PD_NP19-255_AMY_3"  
##  [75] "AA_ASAP112_ctrl_NP16-293_AMY_3"   "AA_ASAP131_PD_NP23-21_AMY_3"     
##  [77] "DA780_ASAP37_PD_NP19-16_AMY_3"    "AA_ASAP114_PD_NP21-57_AMY_3"     
##  [79] "DA778_ASAP31_PD_NP18-117_AMY_3"   "DA791_ASAP50_ctrl_NP18-159_AMY_3"
##  [81] "DA793_ASAP53_ctrl_NP19-36_AMY_3"  "DA801_ASAP53_ctrl_NP19-36_AMY_3" 
##  [83] "DA807_ASAP29_PD_NP17-191_AMY_3"   "DA474_ASAP24_PD_NP16-25_AMY_3"   
##  [85] "AA_ASAP110_ctrl_NP16-119_AMY_3"   "DA805_ASAP56_ctrl_NP19-37_AMY_3" 
##  [87] "AA_ASAP124_ctrl_NP22-37_AMY_3"    "AA_ASAP128_PD_NP21-04_AMY_3"     
##  [89] "AA_ASAP123_ctrl_NP19-218_AMY_3"   "DA512_ASAP60_ctrl_NP19-45_AMY_3" 
##  [91] "AA_ASAP113_ctrl_NP18-148_AMY_3"   "DA778_ASAP31_PD_NP18-117_AMY_5"  
##  [93] "AA_ASAP131_PD_NP23-21_AMY_5"      "DA800_ASAP20_PD_NP16-160_AMY_5"  
##  [95] "AA_ASAP114_PD_NP21-57_AMY_5"      "AA_ASAP113_ctrl_NP18-148_AMY_5"  
##  [97] "ASAP122_PD_NP19-91_AMY_5"         "DA791_ASAP50_ctrl_NP18-159_AMY_5"
##  [99] "DA793_ASAP53_ctrl_NP19-36_AMY_5"  "DA474_ASAP24_PD_NP16-25_AMY_5"   
## [101] "DA805_ASAP56_ctrl_NP19-37_AMY_5"  "AA_ASAP109_PD_NP21-217_AMY_5"    
## [103] "DA802_ASAP40_PD_NP19-23_AMY_5"    "AA_ASAP121_PD_NP17-232_AMY_5"    
## [105] "AA_ASAP124_ctrl_NP22-37_AMY_5"    "DA811_ASAP18_PD_NP16-140_AMY_5"  
## [107] "DA814_ASAP35_PD_NP18-304_AMY_5"   "DA779_ASAP33_PD_NP18-287_AMY_5"  
## [109] "AA_ASAP115_PD_NP21-208_AMY_5"     "AA_ASAP126_PD_NP19-137_AMY_5"    
## [111] "DA512_ASAP60_ctrl_NP19-45_AMY_5"  "AA_ASAP110_ctrl_NP16-119_AMY_5"  
## [113] "DA783_ASAP45_PD_NP19-255_AMY_5"   "DA803_ASAP48_ctrl_NP17-256_AMY_5"
## [115] "AA_ASAP120_PD_NP16-285_AMY_5"     "DA807_ASAP29_PD_NP17-191_AMY_5"  
## [117] "DA780_ASAP37_PD_NP19-16_AMY_5"    "DA801_ASAP53_ctrl_NP19-36_AMY_5" 
## [119] "AA_ASAP123_ctrl_NP19-218_AMY_5"   "AA_ASAP112_ctrl_NP16-293_AMY_5"  
## [121] "AA_ASAP119_PD_NP22-55_AMY_5"      "AA_ASAP128_PD_NP21-04_AMY_5"     
## [123] "DA815_ASAP37_PD_NP19-16_AMY_5"    "DA802_ASAP40_PD_NP19-23_AMY_4"   
## [125] "AA_ASAP112_ctrl_NP16-293_AMY_4"   "DA512_ASAP60_ctrl_NP19-45_AMY_4" 
## [127] "AA_ASAP126_PD_NP19-137_AMY_4"     "AA_ASAP115_PD_NP21-208_AMY_4"    
## [129] "AA_ASAP131_PD_NP23-21_AMY_4"      "DA783_ASAP45_PD_NP19-255_AMY_4"  
## [131] "DA811_ASAP18_PD_NP16-140_AMY_4"   "DA805_ASAP56_ctrl_NP19-37_AMY_4" 
## [133] "DA474_ASAP24_PD_NP16-25_AMY_4"    "AA_ASAP119_PD_NP22-55_AMY_4"     
## [135] "DA801_ASAP53_ctrl_NP19-36_AMY_4"  "DA793_ASAP53_ctrl_NP19-36_AMY_4" 
## [137] "AA_ASAP110_ctrl_NP16-119_AMY_4"   "DA791_ASAP50_ctrl_NP18-159_AMY_4"
## [139] "DA807_ASAP29_PD_NP17-191_AMY_4"   "DA778_ASAP31_PD_NP18-117_AMY_4"  
## [141] "AA_ASAP114_PD_NP21-57_AMY_4"      "AA_ASAP123_ctrl_NP19-218_AMY_4"  
## [143] "AA_ASAP113_ctrl_NP18-148_AMY_4"   "AA_ASAP123_ctrl_NP19-218_AMY_6"  
## 
## $order_rows
##   [1] "HERV_dup773"  "HERV_dup1758" "HERV_dup288"  "HERV_dup1"    "HERV_dup3252"
##   [6] "HERV_dup152"  "HERV_dup2491" "HERV_dup1708" "HERV_dup3390" "HERV_dup2856"
##  [11] "HERV_dup1281" "HERV_dup1209" "HERV_dup265"  "HERV_dup600"  "HERV_dup2966"
##  [16] "HERV_dup302"  "HERV_dup2841" "HERV_dup1079" "HERV_dup2838" "HERV_dup799" 
##  [21] "HERV_dup3357" "HERV_dup926"  "HERV_dup1702" "HERV_dup1050" "HERV_dup614" 
##  [26] "HERV_dup2880" "HERV_dup1000" "HERV_dup631"  "HERV_dup470"  "HERV_dup3226"
##  [31] "HERV_dup384"  "HERV_dup2273" "HERV_dup54"   "HERV_dup1283" "HERV_dup940" 
##  [36] "HERV_dup2900" "HERV_dup1456" "HERV_dup1669" "HERV_dup2381" "HERV_dup293" 
##  [41] "HERV_dup1339" "HERV_dup1888" "HERV_dup2789" "HERV_dup1357" "HERV_dup3266"
##  [46] "HERV_dup379"  "HERV_dup1359" "HERV_dup3171" "HERV_dup209"  "HERV_dup2365"
##  [51] "HERV_dup1102" "HERV_dup112"  "HERV_dup1598" "HERV_dup980"  "HERV_dup1356"
##  [56] "HERV_dup93"   "HERV_dup717"  "HERV_dup417"  "HERV_dup1657" "HERV_dup3363"
##  [61] "HERV_dup3174" "HERV_dup2376" "HERV_dup3105" "HERV_dup1002" "HERV_dup3379"
##  [66] "HERV_dup831"  "HERV_dup3423" "HERV_dup1004" "HERV_dup562"  "HERV_dup1309"
##  [71] "HERV_dup2840" "HERV_dup474"  "HERV_dup1308" "HERV_dup873"  "HERV_dup2182"
##  [76] "HERV_dup1203" "HERV_dup1310" "HERV_dup1701" "HERV_dup3343" "HERV_dup1667"
##  [81] "HERV_dup916"  "HERV_dup518"  "HERV_dup904"  "HERV_dup3375" "HERV_dup612" 
##  [86] "HERV_dup1382" "HERV_dup1362" "HERV_dup1319" "HERV_dup2012" "HERV_dup2299"
##  [91] "HERV_dup1934" "HERV_dup1670" "HERV_dup670"  "HERV_dup37"   "HERV_dup1048"
##  [96] "HERV_dup2106" "HERV_dup1255" "HERV_dup731"  "HERV_dup1345" "HERV_dup2879"
## [101] "HERV_dup1449" "HERV_dup1315" "HERV_dup1334" "HERV_dup443"  "HERV_dup1755"
## [106] "HERV_dup1052" "HERV_dup151"  "HERV_dup3107" "HERV_dup1272" "HERV_dup1447"
## [111] "HERV_dup2217" "HERV_dup2292" "HERV_dup1694" "HERV_dup3522" "HERV_dup3355"
## [116] "HERV_dup966"  "HERV_dup1282" "HERV_dup1307" "HERV_dup2176" "HERV_dup110" 
## [121] "HERV_dup1512" "HERV_dup1371" "HERV_dup2843" "HERV_dup565"  "HERV_dup1750"
## [126] "HERV_dup899"  "HERV_dup1611" "HERV_dup301"  "HERV_dup348"  "HERV_dup1017"
## [131] "HERV_dup1208" "HERV_dup2914" "HERV_dup682"  "HERV_dup913"  "HERV_dup1846"
## [136] "HERV_dup2631" "HERV_dup292"  "HERV_dup57"   "HERV_dup872"  "HERV_dup1663"
## [141] "HERV_dup482"  "HERV_dup369"  "HERV_dup758"  "HERV_dup1001" "HERV_dup2530"
## [146] "HERV_dup2163" "HERV_dup2603" "HERV_dup1046" "HERV_dup3430" "HERV_dup880" 
## [151] "HERV_dup597"  "HERV_dup2902" "HERV_dup3140" "HERV_dup1875" "HERV_dup969" 
## [156] "HERV_dup2261" "HERV_dup2550" "HERV_dup1596" "HERV_dup2438" "HERV_dup3417"
## [161] "HERV_dup1107" "HERV_dup939"  "HERV_dup2599" "HERV_dup1613" "HERV_dup3505"
## [166] "HERV_dup1351" "HERV_dup1776" "HERV_dup3050" "HERV_dup26"   "HERV_dup380" 
## [171] "HERV_dup203"  "HERV_dup1232" "HERV_dup1273" "HERV_dup1253" "HERV_dup2412"
## [176] "HERV_dup2589" "HERV_dup3418" "HERV_dup2847" "HERV_dup2111" "HERV_dup979" 
## [181] "HERV_dup1662" "HERV_dup2963" "HERV_dup3529" "HERV_dup2235" "HERV_dup2961"
## [186] "HERV_dup2566" "HERV_dup1303" "HERV_dup2643" "HERV_dup2662" "HERV_dup5"   
## [191] "HERV_dup2752" "HERV_dup954"  "HERV_dup487"  "HERV_dup18"   "HERV_dup65"  
## [196] "HERV_dup1243" "HERV_dup34"   "HERV_dup2391" "HERV_dup1112" "HERV_dup1081"
## [201] "HERV_dup433"  "HERV_dup1940" "HERV_dup2476" "HERV_dup1569" "HERV_dup468" 
## [206] "HERV_dup1242" "HERV_dup3580" "HERV_dup956"  "HERV_dup1703" "HERV_dup356" 
## [211] "HERV_dup1269" "HERV_dup1358" "HERV_dup2719" "HERV_dup3196" "HERV_dup573" 
## [216] "HERV_dup2166" "HERV_dup3694" "HERV_dup118"  "HERV_dup290"  "HERV_dup1416"
## [221] "HERV_dup3227" "HERV_dup1935" "HERV_dup1036" "HERV_dup1780" "HERV_dup355" 
## [226] "HERV_dup949"  "HERV_dup2266" "HERV_dup1302" "HERV_dup1661" "HERV_dup2857"
## [231] "HERV_dup94"   "HERV_dup1717" "HERV_dup36"   "HERV_dup2812" "HERV_dup3198"
## [236] "HERV_dup2784" "HERV_dup3033" "HERV_dup1331" "HERV_dup1007" "HERV_dup1605"
## [241] "HERV_dup1917" "HERV_dup2607" "HERV_dup2878" "HERV_dup218"  "HERV_dup613" 
## [246] "HERV_dup1500" "HERV_dup1213" "HERV_dup2183" "HERV_dup1749" "HERV_dup1847"
## [251] "HERV_dup2778" "HERV_dup1756" "HERV_dup471"  "HERV_dup1932" "HERV_dup2834"
## [256] "HERV_dup1707" "HERV_dup2250" "HERV_dup3251" "HERV_dup3187" "HERV_dup2561"
## [261] "HERV_dup27"   "HERV_dup329"  "HERV_dup1555" "HERV_dup2366" "HERV_dup2112"
## [266] "HERV_dup1484" "HERV_dup1982" "HERV_dup2939" "HERV_dup202"  "HERV_dup2623"
## [271] "HERV_dup3342" "HERV_dup927"  "HERV_dup2422" "HERV_dup29"   "HERV_dup1617"
## [276] "HERV_dup2823" "HERV_dup2085" "HERV_dup3358" "HERV_dup3270" "HERV_dup3063"
## [281] "HERV_dup2801" "HERV_dup2936" "HERV_dup282"  "HERV_dup3013" "HERV_dup214" 
## [286] "HERV_dup1073" "HERV_dup2769" "HERV_dup2877" "HERV_dup3143" "HERV_dup3020"
## [291] "HERV_dup990"  "HERV_dup3406" "HERV_dup2941" "HERV_dup3124" "HERV_dup399" 
## [296] "HERV_dup1720" "HERV_dup1730" "HERV_dup586"  "HERV_dup108"  "HERV_dup1268"
## [301] "HERV_dup2188" "HERV_dup1394" "HERV_dup2264" "HERV_dup1089" "HERV_dup2480"
## [306] "HERV_dup1298" "HERV_dup1920" "HERV_dup1240" "HERV_dup2353" "HERV_dup632" 
## [311] "HERV_dup2736" "HERV_dup2964" "HERV_dup1071" "HERV_dup1802" "HERV_dup1297"
## [316] "HERV_dup1453" "HERV_dup554"  "HERV_dup251"  "HERV_dup1972" "HERV_dup120" 
## [321] "HERV_dup1869" "HERV_dup314"  "HERV_dup1316" "HERV_dup661"  "HERV_dup1390"
## [326] "HERV_dup2319" "HERV_dup2598" "HERV_dup968"  "HERV_dup2785" "HERV_dup1236"
## [331] "HERV_dup2915" "HERV_dup488"  "HERV_dup1931" "HERV_dup2379" "HERV_dup3410"
## [336] "HERV_dup3365" "HERV_dup2695" "HERV_dup1731" "HERV_dup2093" "HERV_dup3408"
## [341] "HERV_dup3239" "HERV_dup1890" "HERV_dup2949" "HERV_dup1557" "HERV_dup2896"
## [346] "HERV_dup3319" "HERV_dup58"   "HERV_dup890"  "HERV_dup2436" "HERV_dup2803"
## [351] "HERV_dup2149" "HERV_dup3231" "HERV_dup2962" "HERV_dup746"  "HERV_dup626" 
## [356] "HERV_dup1324" "HERV_dup876"  "HERV_dup1321" "HERV_dup2533" "HERV_dup2383"
## [361] "HERV_dup3507" "HERV_dup2415" "HERV_dup1295" "HERV_dup2129" "HERV_dup1437"
## [366] "HERV_dup350"  "HERV_dup215"  "HERV_dup3388" "HERV_dup662"  "HERV_dup467" 
## [371] "HERV_dup3341" "HERV_dup2733" "HERV_dup249"  "HERV_dup517"  "HERV_dup1494"
## [376] "HERV_dup1374" "HERV_dup1587" "HERV_dup3286" "HERV_dup3148" "HERV_dup409" 
## [381] "HERV_dup377"  "HERV_dup1556" "HERV_dup2588" "HERV_dup441"  "HERV_dup967" 
## [386] "HERV_dup2529" "HERV_dup729"  "HERV_dup1973" "HERV_dup2735" "HERV_dup2646"
## [391] "HERV_dup1532" "HERV_dup2500" "HERV_dup2653" "HERV_dup2555" "HERV_dup386" 
## [396] "HERV_dup2772" "HERV_dup3351" "HERV_dup2651" "HERV_dup982"  "HERV_dup1187"
## [401] "HERV_dup1093" "HERV_dup2192" "HERV_dup1640" "HERV_dup1655" "HERV_dup1317"
## [406] "HERV_dup3366" "HERV_dup851"  "HERV_dup1658" "HERV_dup3118" "HERV_dup3037"
## [411] "HERV_dup1228" "HERV_dup3220" "HERV_dup2739" "HERV_dup1851" "HERV_dup1953"
## [416] "HERV_dup2158" "HERV_dup3108" "HERV_dup665"  "HERV_dup2242" "HERV_dup1005"
## [421] "HERV_dup2298" "HERV_dup2179" "HERV_dup777"  "HERV_dup591"  "HERV_dup599" 
## [426] "HERV_dup3100" "HERV_dup2562" "HERV_dup180"  "HERV_dup357"  "HERV_dup1029"
## [431] "HERV_dup1653" "HERV_dup1491" "HERV_dup1671" "HERV_dup2696" "HERV_dup3416"
## [436] "HERV_dup23"   "HERV_dup2905" "HERV_dup2886" "HERV_dup1080" "HERV_dup928" 
## [441] "HERV_dup3217" "HERV_dup1719" "HERV_dup1433" "HERV_dup2481" "HERV_dup3328"
## [446] "HERV_dup577"  "HERV_dup2747" "HERV_dup2977" "HERV_dup2848" "HERV_dup2604"
## [451] "HERV_dup331"  "HERV_dup1366" "HERV_dup508"  "HERV_dup2033" "HERV_dup710" 
## [456] "HERV_dup2730" "HERV_dup1614" "HERV_dup934"  "HERV_dup551"  "HERV_dup469" 
## [461] "HERV_dup115"  "HERV_dup1210" "HERV_dup3212" "HERV_dup2272" "HERV_dup1389"
## [466] "HERV_dup1804" "HERV_dup2337" "HERV_dup1384" "HERV_dup492"  "HERV_dup3394"
## [471] "HERV_dup1440" "HERV_dup1038" "HERV_dup1222" "HERV_dup1064" "HERV_dup419" 
## [476] "HERV_dup2632" "HERV_dup2187" "HERV_dup2034" "HERV_dup1668" "HERV_dup1285"
## [481] "HERV_dup1520" "HERV_dup1156" "HERV_dup2620" "HERV_dup852"  "HERV_dup1438"
## [486] "HERV_dup2891" "HERV_dup1889" "HERV_dup300"  "HERV_dup900"  "HERV_dup732" 
## [491] "HERV_dup1937" "HERV_dup3044" "HERV_dup2978" "HERV_dup870"  "HERV_dup38"  
## [496] "HERV_dup1496" "HERV_dup1926" "HERV_dup2303" "HERV_dup1013" "HERV_dup1201"
## [501] "HERV_dup3673" "HERV_dup909"  "HERV_dup1914" "HERV_dup894"  "HERV_dup975" 
## [506] "HERV_dup2655" "HERV_dup1923" "HERV_dup272"  "HERV_dup723"  "HERV_dup2027"
## [511] "HERV_dup739"  "HERV_dup2130" "HERV_dup3248" "HERV_dup336"  "HERV_dup2137"
## [516] "HERV_dup2680" "HERV_dup1047" "HERV_dup2282" "HERV_dup2706" "HERV_dup1513"
## [521] "HERV_dup2804" "HERV_dup2663" "HERV_dup2524" "HERV_dup173"  "HERV_dup3335"
## [526] "HERV_dup127"  "HERV_dup1724" "HERV_dup1212" "HERV_dup2041" "HERV_dup933" 
## [531] "HERV_dup3459" "HERV_dup1350" "HERV_dup1278" "HERV_dup1381" "HERV_dup3008"
## [536] "HERV_dup194"  "HERV_dup61"   "HERV_dup1378" "HERV_dup2378" "HERV_dup388" 
## [541] "HERV_dup250"  "HERV_dup2647" "HERV_dup344"  "HERV_dup3688" "HERV_dup1304"
## [546] "HERV_dup1090" "HERV_dup1114" "HERV_dup3215" "HERV_dup1891" "HERV_dup519" 
## [551] "HERV_dup553"  "HERV_dup2019" "HERV_dup243"  "HERV_dup184"  "HERV_dup2934"
## [556] "HERV_dup1541" "HERV_dup2536" "HERV_dup2128" "HERV_dup3117" "HERV_dup2404"
## [561] "HERV_dup1962" "HERV_dup977"  "HERV_dup1103" "HERV_dup3284" "HERV_dup3481"
## [566] "HERV_dup2141" "HERV_dup2809" "HERV_dup1979" "HERV_dup277"  "HERV_dup461" 
## [571] "HERV_dup3210" "HERV_dup1279" "HERV_dup884"  "HERV_dup1235" "HERV_dup39"  
## [576] "HERV_dup1412" "HERV_dup736"  "HERV_dup1948" "HERV_dup935"  "HERV_dup434" 
## [581] "HERV_dup2985" "HERV_dup882"  "HERV_dup2797" "HERV_dup570"  "HERV_dup2635"
## [586] "HERV_dup1579" "HERV_dup3131" "HERV_dup2002" "HERV_dup1902" "HERV_dup1195"
## [591] "HERV_dup1248" "HERV_dup1218" "HERV_dup803"  "HERV_dup724"  "HERV_dup2278"
## [596] "HERV_dup2937" "HERV_dup578"  "HERV_dup1383" "HERV_dup276"  "HERV_dup2134"
## [601] "HERV_dup1129" "HERV_dup1527" "HERV_dup556"  "HERV_dup2907" "HERV_dup3519"
## [606] "HERV_dup2548" "HERV_dup2855" "HERV_dup1082" "HERV_dup1049" "HERV_dup1526"
## [611] "HERV_dup505"  "HERV_dup321"  "HERV_dup1470" "HERV_dup2728" "HERV_dup86"  
## [616] "HERV_dup1778" "HERV_dup21"   "HERV_dup1413" "HERV_dup2100" "HERV_dup568" 
## [621] "HERV_dup1638" "HERV_dup2334" "HERV_dup1364" "HERV_dup530"  "HERV_dup1629"
## [626] "HERV_dup1333" "HERV_dup1254" "HERV_dup2602" "HERV_dup84"   "HERV_dup1245"
## [631] "HERV_dup776"  "HERV_dup1417" "HERV_dup1401" "HERV_dup2290" "HERV_dup2320"
## [636] "HERV_dup3031" "HERV_dup3179" "HERV_dup692"  "HERV_dup3287" "HERV_dup2152"
## [641] "HERV_dup2979" "HERV_dup572"  "HERV_dup1944" "HERV_dup3182" "HERV_dup2159"
## [646] "HERV_dup185"  "HERV_dup3073" "HERV_dup728"  "HERV_dup1014" "HERV_dup1757"
## [651] "HERV_dup735"  "HERV_dup1108" "HERV_dup671"  "HERV_dup407"  "HERV_dup240" 
## [656] "HERV_dup17"   "HERV_dup291"  "HERV_dup201"  "HERV_dup1933" "HERV_dup595" 
## [661] "HERV_dup703"  "HERV_dup2518" "HERV_dup1184" "HERV_dup1182" "HERV_dup1872"
## [666] "HERV_dup446"  "HERV_dup1664" "HERV_dup1711" "HERV_dup1131" "HERV_dup2482"
## [671] "HERV_dup634"  "HERV_dup1099" "HERV_dup1327" "HERV_dup133"  "HERV_dup509" 
## [676] "HERV_dup1459" "HERV_dup2942" "HERV_dup3181" "HERV_dup772"  "HERV_dup177" 
## [681] "HERV_dup1346" "HERV_dup2945" "HERV_dup183"  "HERV_dup2356" "HERV_dup1146"
## [686] "HERV_dup1673" "HERV_dup2967" "HERV_dup981"  "HERV_dup78"   "HERV_dup3154"
## [691] "HERV_dup450"  "HERV_dup1403" "HERV_dup1003" "HERV_dup381"  "HERV_dup2972"
## [696] "HERV_dup2441" "HERV_dup1549" "HERV_dup2557" "HERV_dup930"  "HERV_dup2894"
## [701] "HERV_dup846"  "HERV_dup1322" "HERV_dup3219" "HERV_dup3137" "HERV_dup1943"
## [706] "HERV_dup1656" "HERV_dup1823" "HERV_dup2525" "HERV_dup452"  "HERV_dup2464"
## [711] "HERV_dup1639" "HERV_dup1868" "HERV_dup447"  "HERV_dup3588" "HERV_dup129" 
## [716] "HERV_dup1752" "HERV_dup1514" "HERV_dup3606" "HERV_dup3016" "HERV_dup389" 
## [721] "HERV_dup1239" "HERV_dup924"  "HERV_dup1415" "HERV_dup2324" "HERV_dup398" 
## [726] "HERV_dup1733" "HERV_dup2897" "HERV_dup850"  "HERV_dup640"  "HERV_dup2875"
## [731] "HERV_dup3189" "HERV_dup3545" "HERV_dup1958" "HERV_dup3015" "HERV_dup2479"
## [736] "HERV_dup400"  "HERV_dup1172" "HERV_dup2743" "HERV_dup3607"

asap_heatmap_snRNA(region = c("SN"), 
                   tes = data_TE_annotation[which(data_TE_annotation$type == "HERV"),"TE_id"], 
                   return_df = F, 
                   breaks = seq(0,15,length.out = 52), 
                   data = TE_data, 
                   group_cols = c("celltype"), 
                   index_row_reorder = c(HERVs_sorted_sn),
                   order_cols_groups = order_cols_celltype,
                   title = "SN HERV: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
                   annotation_cols = annotation_cols)

## $heatmap
## 
## $order_cols
##   [1] "AA_ASAP129_ctrl_NP22-37_SN_1"    "AA_ASAP118_PD_NP22-55_SN_1"     
##   [3] "DA792_ASAP51_ctrl_NP19-36_SN_1"  "AA_ASAP137_PD_NP23-21_SN_1"     
##   [5] "DA487_ASAP8_ctrl_PT231_SN_1"     "AA_ASAP133_PD_NP17-232_SN_2"    
##   [7] "AA_ASAP99_ctrl_NP16-284_SN_2"    "DA784_ASAP46_ctrl_NP17-256_SN_2"
##   [9] "DA431_ASAP4_PD_P74_SN_2"         "DA479_ASAP7_ctrl_NP16-21_SN_2"  
##  [11] "AA_ASAP137_PD_NP23-21_SN_2"      "DA794_ASAP54_ctrl_NP19-37_SN_2" 
##  [13] "AA_ASAP132_PD_NP16-285_SN_2"     "DA433_ASAP5_ctrl_NP16-161_SN_2" 
##  [15] "DA475_ASAP2_PD_NP16-25_SN_2"     "AA_ASAP129_ctrl_NP22-37_SN_2"   
##  [17] "AA_ASAP118_PD_NP22-55_SN_2"      "DA782_ASAP41_PD_NP19-108_SN_2"  
##  [19] "AA_ASAP108_ctrl_NP18-148_SN_2"   "MJ_ASAP6_ctrl_NP16-164_SN_2"    
##  [21] "DA487_ASAP8_ctrl_PT231_SN_2"     "AA_ASAP104_ctrl_NP16-119_SN_2"  
##  [23] "DA429_ASAP1_PD_NP16-162_SN_2"    "AA_ASAP135_PD_NP19-137_SN_2"    
##  [25] "AA_ASAP134_PD_NP19-91_SN_2"      "DA473_ASAP38_PD_NP19-23_SN_2"   
##  [27] "AA_ASAP105_ctrl_NP16-293_SN_2"   "DA796_ASAP57_ctrl_NP19-45_SN_2" 
##  [29] "AA_ASAP127_ctrl_NP19-218_SN_2"   "DA792_ASAP51_ctrl_NP19-36_SN_2" 
##  [31] "AA_ASAP101_PD_NP21-57_SN_2"      "AA_ASAP102_PD_NP21-208_SN_2"    
##  [33] "DA489_ASAP3_PD_P73_SN_2"         "AA_ASAP103_PD_NP21-217_SN_2"    
##  [35] "DA511_ASAP21_PD_NP16-269_SN_2"   "DA784_ASAP46_ctrl_NP17-256_SN_3"
##  [37] "AA_ASAP99_ctrl_NP16-284_SN_3"    "AA_ASAP134_PD_NP19-91_SN_3"     
##  [39] "DA433_ASAP5_ctrl_NP16-161_SN_3"  "AA_ASAP129_ctrl_NP22-37_SN_3"   
##  [41] "DA431_ASAP4_PD_P74_SN_3"         "AA_ASAP127_ctrl_NP19-218_SN_3"  
##  [43] "AA_ASAP136_PD_NP21-04_SN_3"      "AA_ASAP133_PD_NP17-232_SN_3"    
##  [45] "AA_ASAP104_ctrl_NP16-119_SN_3"   "DA796_ASAP57_ctrl_NP19-45_SN_3" 
##  [47] "DA479_ASAP7_ctrl_NP16-21_SN_3"   "AA_ASAP101_PD_NP21-57_SN_3"     
##  [49] "DA489_ASAP3_PD_P73_SN_3"         "DA792_ASAP51_ctrl_NP19-36_SN_3" 
##  [51] "DA475_ASAP2_PD_NP16-25_SN_3"     "AA_ASAP137_PD_NP23-21_SN_3"     
##  [53] "AA_ASAP135_PD_NP19-137_SN_3"     "DA511_ASAP21_PD_NP16-269_SN_3"  
##  [55] "DA782_ASAP41_PD_NP19-108_SN_3"   "DA794_ASAP54_ctrl_NP19-37_SN_3" 
##  [57] "AA_ASAP102_PD_NP21-208_SN_3"     "AA_ASAP103_PD_NP21-217_SN_3"    
##  [59] "AA_ASAP105_ctrl_NP16-293_SN_3"   "DA473_ASAP38_PD_NP19-23_SN_3"   
##  [61] "AA_ASAP108_ctrl_NP18-148_SN_3"   "MJ_ASAP6_ctrl_NP16-164_SN_3"    
##  [63] "AA_ASAP132_PD_NP16-285_SN_3"     "DA429_ASAP1_PD_NP16-162_SN_3"   
##  [65] "AA_ASAP118_PD_NP22-55_SN_3"      "DA487_ASAP8_ctrl_PT231_SN_3"    
##  [67] "AA_ASAP99_ctrl_NP16-284_SN_5"    "AA_ASAP105_ctrl_NP16-293_SN_5"  
##  [69] "DA784_ASAP46_ctrl_NP17-256_SN_5" "AA_ASAP132_PD_NP16-285_SN_5"    
##  [71] "AA_ASAP102_PD_NP21-208_SN_5"     "DA433_ASAP5_ctrl_NP16-161_SN_5" 
##  [73] "AA_ASAP108_ctrl_NP18-148_SN_5"   "DA473_ASAP38_PD_NP19-23_SN_5"   
##  [75] "MJ_ASAP6_ctrl_NP16-164_SN_5"     "AA_ASAP127_ctrl_NP19-218_SN_5"  
##  [77] "AA_ASAP129_ctrl_NP22-37_SN_5"    "DA431_ASAP4_PD_P74_SN_5"        
##  [79] "AA_ASAP136_PD_NP21-04_SN_5"      "AA_ASAP104_ctrl_NP16-119_SN_5"  
##  [81] "DA475_ASAP2_PD_NP16-25_SN_5"     "DA489_ASAP3_PD_P73_SN_5"        
##  [83] "AA_ASAP101_PD_NP21-57_SN_5"      "AA_ASAP103_PD_NP21-217_SN_5"    
##  [85] "DA511_ASAP21_PD_NP16-269_SN_5"   "AA_ASAP135_PD_NP19-137_SN_5"    
##  [87] "DA792_ASAP51_ctrl_NP19-36_SN_5"  "DA794_ASAP54_ctrl_NP19-37_SN_5" 
##  [89] "DA782_ASAP41_PD_NP19-108_SN_5"   "AA_ASAP137_PD_NP23-21_SN_5"     
##  [91] "AA_ASAP118_PD_NP22-55_SN_5"      "DA429_ASAP1_PD_NP16-162_SN_5"   
##  [93] "AA_ASAP134_PD_NP19-91_SN_5"      "AA_ASAP133_PD_NP17-232_SN_5"    
##  [95] "DA479_ASAP7_ctrl_NP16-21_SN_5"   "DA796_ASAP57_ctrl_NP19-45_SN_5" 
##  [97] "DA487_ASAP8_ctrl_PT231_SN_5"     "AA_ASAP134_PD_NP19-91_SN_4"     
##  [99] "DA473_ASAP38_PD_NP19-23_SN_4"    "AA_ASAP129_ctrl_NP22-37_SN_4"   
## [101] "DA431_ASAP4_PD_P74_SN_4"         "MJ_ASAP6_ctrl_NP16-164_SN_4"    
## [103] "AA_ASAP118_PD_NP22-55_SN_4"      "AA_ASAP108_ctrl_NP18-148_SN_4"  
## [105] "DA433_ASAP5_ctrl_NP16-161_SN_4"  "AA_ASAP102_PD_NP21-208_SN_4"    
## [107] "DA489_ASAP3_PD_P73_SN_4"         "DA511_ASAP21_PD_NP16-269_SN_4"  
## [109] "AA_ASAP127_ctrl_NP19-218_SN_4"   "AA_ASAP101_PD_NP21-57_SN_4"     
## [111] "AA_ASAP103_PD_NP21-217_SN_4"     "DA475_ASAP2_PD_NP16-25_SN_4"    
## [113] "AA_ASAP104_ctrl_NP16-119_SN_4"   "DA794_ASAP54_ctrl_NP19-37_SN_4" 
## [115] "DA487_ASAP8_ctrl_PT231_SN_4"     "DA782_ASAP41_PD_NP19-108_SN_4"  
## [117] "AA_ASAP137_PD_NP23-21_SN_4"      "DA429_ASAP1_PD_NP16-162_SN_4"   
## [119] "AA_ASAP135_PD_NP19-137_SN_4"     "DA792_ASAP51_ctrl_NP19-36_SN_4" 
## [121] "AA_ASAP133_PD_NP17-232_SN_4"     "DA792_ASAP51_ctrl_NP19-36_SN_6" 
## [123] "AA_ASAP137_PD_NP23-21_SN_6"      "AA_ASAP133_PD_NP17-232_SN_7"    
## [125] "AA_ASAP108_ctrl_NP18-148_SN_7"   "AA_ASAP137_PD_NP23-21_SN_7"     
## 
## $order_rows
##   [1] "HERV_dup773"  "HERV_dup1758" "HERV_dup1"    "HERV_dup2491" "HERV_dup288" 
##   [6] "HERV_dup2856" "HERV_dup1281" "HERV_dup1209" "HERV_dup2966" "HERV_dup3390"
##  [11] "HERV_dup1708" "HERV_dup926"  "HERV_dup799"  "HERV_dup1050" "HERV_dup302" 
##  [16] "HERV_dup940"  "HERV_dup265"  "HERV_dup600"  "HERV_dup1702" "HERV_dup3252"
##  [21] "HERV_dup2900" "HERV_dup2838" "HERV_dup2880" "HERV_dup3357" "HERV_dup1079"
##  [26] "HERV_dup2841" "HERV_dup2603" "HERV_dup2273" "HERV_dup1339" "HERV_dup152" 
##  [31] "HERV_dup54"   "HERV_dup1283" "HERV_dup1000" "HERV_dup1356" "HERV_dup470" 
##  [36] "HERV_dup2789" "HERV_dup3105" "HERV_dup1357" "HERV_dup1888" "HERV_dup379" 
##  [41] "HERV_dup1669" "HERV_dup1036" "HERV_dup93"   "HERV_dup1456" "HERV_dup1002"
##  [46] "HERV_dup980"  "HERV_dup614"  "HERV_dup2376" "HERV_dup1359" "HERV_dup1598"
##  [51] "HERV_dup562"  "HERV_dup2381" "HERV_dup2879" "HERV_dup1004" "HERV_dup3379"
##  [56] "HERV_dup2365" "HERV_dup1657" "HERV_dup1102" "HERV_dup717"  "HERV_dup3226"
##  [61] "HERV_dup112"  "HERV_dup2182" "HERV_dup2292" "HERV_dup2902" "HERV_dup209" 
##  [66] "HERV_dup2299" "HERV_dup474"  "HERV_dup3423" "HERV_dup34"   "HERV_dup1308"
##  [71] "HERV_dup966"  "HERV_dup3266" "HERV_dup417"  "HERV_dup1052" "HERV_dup1701"
##  [76] "HERV_dup1203" "HERV_dup3171" "HERV_dup3174" "HERV_dup3375" "HERV_dup1309"
##  [81] "HERV_dup1334" "HERV_dup1310" "HERV_dup3343" "HERV_dup2217" "HERV_dup731" 
##  [86] "HERV_dup1934" "HERV_dup873"  "HERV_dup1667" "HERV_dup2530" "HERV_dup2012"
##  [91] "HERV_dup612"  "HERV_dup1255" "HERV_dup1007" "HERV_dup1319" "HERV_dup3363"
##  [96] "HERV_dup1362" "HERV_dup3522" "HERV_dup904"  "HERV_dup384"  "HERV_dup597" 
## [101] "HERV_dup1382" "HERV_dup1875" "HERV_dup3013" "HERV_dup758"  "HERV_dup1345"
## [106] "HERV_dup3418" "HERV_dup301"  "HERV_dup1670" "HERV_dup3694" "HERV_dup518" 
## [111] "HERV_dup1755" "HERV_dup880"  "HERV_dup2840" "HERV_dup2589" "HERV_dup110" 
## [116] "HERV_dup2438" "HERV_dup2643" "HERV_dup2914" "HERV_dup151"  "HERV_dup1282"
## [121] "HERV_dup37"   "HERV_dup899"  "HERV_dup1663" "HERV_dup3107" "HERV_dup1611"
## [126] "HERV_dup1447" "HERV_dup916"  "HERV_dup2752" "HERV_dup203"  "HERV_dup1001"
## [131] "HERV_dup2843" "HERV_dup2261" "HERV_dup2192" "HERV_dup2847" "HERV_dup1449"
## [136] "HERV_dup3355" "HERV_dup2631" "HERV_dup118"  "HERV_dup3020" "HERV_dup1048"
## [141] "HERV_dup57"   "HERV_dup1315" "HERV_dup1017" "HERV_dup292"  "HERV_dup1846"
## [146] "HERV_dup1358" "HERV_dup1940" "HERV_dup2106" "HERV_dup1776" "HERV_dup1253"
## [151] "HERV_dup1694" "HERV_dup2891" "HERV_dup2111" "HERV_dup3050" "HERV_dup18"  
## [156] "HERV_dup2550" "HERV_dup2415" "HERV_dup3231" "HERV_dup1351" "HERV_dup1512"
## [161] "HERV_dup1750" "HERV_dup954"  "HERV_dup5"    "HERV_dup1302" "HERV_dup967" 
## [166] "HERV_dup2481" "HERV_dup2320" "HERV_dup2588" "HERV_dup1107" "HERV_dup979" 
## [171] "HERV_dup2784" "HERV_dup1240" "HERV_dup1374" "HERV_dup1242" "HERV_dup661" 
## [176] "HERV_dup573"  "HERV_dup380"  "HERV_dup670"  "HERV_dup1662" "HERV_dup2961"
## [181] "HERV_dup482"  "HERV_dup1596" "HERV_dup356"  "HERV_dup599"  "HERV_dup467" 
## [186] "HERV_dup3198" "HERV_dup2129" "HERV_dup1243" "HERV_dup2176" "HERV_dup3417"
## [191] "HERV_dup355"  "HERV_dup831"  "HERV_dup1232" "HERV_dup65"   "HERV_dup2936"
## [196] "HERV_dup2834" "HERV_dup290"  "HERV_dup872"  "HERV_dup1720" "HERV_dup1269"
## [201] "HERV_dup1071" "HERV_dup3529" "HERV_dup682"  "HERV_dup1081" "HERV_dup956" 
## [206] "HERV_dup509"  "HERV_dup3220" "HERV_dup2235" "HERV_dup1802" "HERV_dup2476"
## [211] "HERV_dup3015" "HERV_dup968"  "HERV_dup2266" "HERV_dup2166" "HERV_dup2877"
## [216] "HERV_dup2179" "HERV_dup1371" "HERV_dup1847" "HERV_dup2041" "HERV_dup913" 
## [221] "HERV_dup3430" "HERV_dup433"  "HERV_dup1569" "HERV_dup1208" "HERV_dup662" 
## [226] "HERV_dup487"  "HERV_dup1187" "HERV_dup1236" "HERV_dup2242" "HERV_dup1484"
## [231] "HERV_dup2183" "HERV_dup471"  "HERV_dup26"   "HERV_dup2733" "HERV_dup94"  
## [236] "HERV_dup3580" "HERV_dup3239" "HERV_dup2412" "HERV_dup1073" "HERV_dup1112"
## [241] "HERV_dup3140" "HERV_dup3187" "HERV_dup1935" "HERV_dup2298" "HERV_dup2163"
## [246] "HERV_dup282"  "HERV_dup939"  "HERV_dup419"  "HERV_dup409"  "HERV_dup890" 
## [251] "HERV_dup2662" "HERV_dup732"  "HERV_dup2566" "HERV_dup2939" "HERV_dup2391"
## [256] "HERV_dup1917" "HERV_dup1931" "HERV_dup2735" "HERV_dup2857" "HERV_dup2719"
## [261] "HERV_dup1272" "HERV_dup108"  "HERV_dup180"  "HERV_dup2188" "HERV_dup1316"
## [266] "HERV_dup1756" "HERV_dup1331" "HERV_dup249"  "HERV_dup1780" "HERV_dup2769"
## [271] "HERV_dup1613" "HERV_dup990"  "HERV_dup293"  "HERV_dup2623" "HERV_dup1459"
## [276] "HERV_dup2812" "HERV_dup3388" "HERV_dup443"  "HERV_dup949"  "HERV_dup2941"
## [281] "HERV_dup1235" "HERV_dup272"  "HERV_dup2085" "HERV_dup1717" "HERV_dup2801"
## [286] "HERV_dup2803" "HERV_dup1213" "HERV_dup173"  "HERV_dup3341" "HERV_dup3519"
## [291] "HERV_dup1661" "HERV_dup1749" "HERV_dup3410" "HERV_dup1303" "HERV_dup1090"
## [296] "HERV_dup1731" "HERV_dup468"  "HERV_dup3408" "HERV_dup3406" "HERV_dup1324"
## [301] "HERV_dup2964" "HERV_dup556"  "HERV_dup202"  "HERV_dup2599" "HERV_dup2379"
## [306] "HERV_dup1089" "HERV_dup1703" "HERV_dup1438" "HERV_dup1297" "HERV_dup3016"
## [311] "HERV_dup2500" "HERV_dup3124" "HERV_dup2383" "HERV_dup626"  "HERV_dup2604"
## [316] "HERV_dup3033" "HERV_dup2598" "HERV_dup876"  "HERV_dup1513" "HERV_dup1889"
## [321] "HERV_dup2963" "HERV_dup3251" "HERV_dup1932" "HERV_dup2366" "HERV_dup1605"
## [326] "HERV_dup1046" "HERV_dup389"  "HERV_dup1719" "HERV_dup2915" "HERV_dup1114"
## [331] "HERV_dup2653" "HERV_dup2736" "HERV_dup3270" "HERV_dup554"  "HERV_dup2158"
## [336] "HERV_dup2533" "HERV_dup2264" "HERV_dup2525" "HERV_dup377"  "HERV_dup2962"
## [341] "HERV_dup1526" "HERV_dup3063" "HERV_dup348"  "HERV_dup1671" "HERV_dup214" 
## [346] "HERV_dup3148" "HERV_dup1587" "HERV_dup3342" "HERV_dup2353" "HERV_dup1416"
## [351] "HERV_dup36"   "HERV_dup2033" "HERV_dup2949" "HERV_dup2728" "HERV_dup1920"
## [356] "HERV_dup1222" "HERV_dup2934" "HERV_dup1496" "HERV_dup183"  "HERV_dup2548"
## [361] "HERV_dup1891" "HERV_dup1617" "HERV_dup1707" "HERV_dup692"  "HERV_dup331" 
## [366] "HERV_dup2250" "HERV_dup3358" "HERV_dup2422" "HERV_dup1245" "HERV_dup613" 
## [371] "HERV_dup1653" "HERV_dup1321" "HERV_dup2480" "HERV_dup300"  "HERV_dup344" 
## [376] "HERV_dup1248" "HERV_dup2905" "HERV_dup729"  "HERV_dup3227" "HERV_dup2878"
## [381] "HERV_dup640"  "HERV_dup2019" "HERV_dup1298" "HERV_dup2027" "HERV_dup58"  
## [386] "HERV_dup710"  "HERV_dup218"  "HERV_dup1730" "HERV_dup3351" "HERV_dup632" 
## [391] "HERV_dup1317" "HERV_dup3287" "HERV_dup1268" "HERV_dup2112" "HERV_dup2632"
## [396] "HERV_dup909"  "HERV_dup3505" "HERV_dup1029" "HERV_dup1156" "HERV_dup2607"
## [401] "HERV_dup772"  "HERV_dup61"   "HERV_dup928"  "HERV_dup2334" "HERV_dup517" 
## [406] "HERV_dup84"   "HERV_dup329"  "HERV_dup933"  "HERV_dup3365" "HERV_dup1972"
## [411] "HERV_dup1201" "HERV_dup1982" "HERV_dup1064" "HERV_dup2907" "HERV_dup3416"
## [416] "HERV_dup1307" "HERV_dup386"  "HERV_dup3507" "HERV_dup1322" "HERV_dup27"  
## [421] "HERV_dup1973" "HERV_dup2436" "HERV_dup2303" "HERV_dup1210" "HERV_dup631" 
## [426] "HERV_dup2848" "HERV_dup1733" "HERV_dup1953" "HERV_dup3100" "HERV_dup882" 
## [431] "HERV_dup927"  "HERV_dup441"  "HERV_dup852"  "HERV_dup2739" "HERV_dup1239"
## [436] "HERV_dup194"  "HERV_dup388"  "HERV_dup1129" "HERV_dup120"  "HERV_dup776" 
## [441] "HERV_dup3118" "HERV_dup565"  "HERV_dup553"  "HERV_dup1279" "HERV_dup1614"
## [446] "HERV_dup1658" "HERV_dup969"  "HERV_dup1494" "HERV_dup519"  "HERV_dup1869"
## [451] "HERV_dup2561" "HERV_dup724"  "HERV_dup1872" "HERV_dup2804" "HERV_dup243" 
## [456] "HERV_dup1579" "HERV_dup2128" "HERV_dup29"   "HERV_dup746"  "HERV_dup2141"
## [461] "HERV_dup736"  "HERV_dup2134" "HERV_dup2555" "HERV_dup2747" "HERV_dup1003"
## [466] "HERV_dup276"  "HERV_dup38"   "HERV_dup2778" "HERV_dup381"  "HERV_dup1366"
## [471] "HERV_dup586"  "HERV_dup1394" "HERV_dup1131" "HERV_dup314"  "HERV_dup1890"
## [476] "HERV_dup21"   "HERV_dup447"  "HERV_dup3394" "HERV_dup1295" "HERV_dup2886"
## [481] "HERV_dup2002" "HERV_dup803"  "HERV_dup1005" "HERV_dup2324" "HERV_dup634" 
## [486] "HERV_dup488"  "HERV_dup321"  "HERV_dup115"  "HERV_dup1285" "HERV_dup934" 
## [491] "HERV_dup2646" "HERV_dup2602" "HERV_dup777"  "HERV_dup1333" "HERV_dup665" 
## [496] "HERV_dup2855" "HERV_dup2635" "HERV_dup291"  "HERV_dup215"  "HERV_dup1541"
## [501] "HERV_dup703"  "HERV_dup434"  "HERV_dup1014" "HERV_dup1778" "HERV_dup884" 
## [506] "HERV_dup1914" "HERV_dup1500" "HERV_dup1948" "HERV_dup975"  "HERV_dup1433"
## [511] "HERV_dup2093" "HERV_dup1384" "HERV_dup1184" "HERV_dup1668" "HERV_dup2772"
## [516] "HERV_dup1724" "HERV_dup3182" "HERV_dup894"  "HERV_dup1390" "HERV_dup870" 
## [521] "HERV_dup2187" "HERV_dup127"  "HERV_dup3143" "HERV_dup2985" "HERV_dup2743"
## [526] "HERV_dup1047" "HERV_dup1417" "HERV_dup469"  "HERV_dup2937" "HERV_dup2152"
## [531] "HERV_dup1413" "HERV_dup578"  "HERV_dup129"  "HERV_dup851"  "HERV_dup2557"
## [536] "HERV_dup3181" "HERV_dup369"  "HERV_dup251"  "HERV_dup3286" "HERV_dup407" 
## [541] "HERV_dup1851" "HERV_dup2319" "HERV_dup2663" "HERV_dup2518" "HERV_dup1038"
## [546] "HERV_dup2282" "HERV_dup551"  "HERV_dup2655" "HERV_dup1412" "HERV_dup1437"
## [551] "HERV_dup1304" "HERV_dup3008" "HERV_dup850"  "HERV_dup728"  "HERV_dup1212"
## [556] "HERV_dup1403" "HERV_dup981"  "HERV_dup2536" "HERV_dup184"  "HERV_dup1453"
## [561] "HERV_dup1093" "HERV_dup1937" "HERV_dup2894" "HERV_dup250"  "HERV_dup2875"
## [566] "HERV_dup723"  "HERV_dup1108" "HERV_dup1923" "HERV_dup3073" "HERV_dup1082"
## [571] "HERV_dup446"  "HERV_dup1555" "HERV_dup185"  "HERV_dup1389" "HERV_dup3137"
## [576] "HERV_dup1958" "HERV_dup3108" "HERV_dup1378" "HERV_dup1350" "HERV_dup1491"
## [581] "HERV_dup2100" "HERV_dup2278" "HERV_dup570"  "HERV_dup1470" "HERV_dup3366"
## [586] "HERV_dup2651" "HERV_dup508"  "HERV_dup2524" "HERV_dup1629" "HERV_dup461" 
## [591] "HERV_dup577"  "HERV_dup1278" "HERV_dup1655" "HERV_dup505"  "HERV_dup2647"
## [596] "HERV_dup2562" "HERV_dup2441" "HERV_dup1381" "HERV_dup1514" "HERV_dup3189"
## [601] "HERV_dup1804" "HERV_dup23"   "HERV_dup3210" "HERV_dup2972" "HERV_dup2034"
## [606] "HERV_dup1273" "HERV_dup2130" "HERV_dup2967" "HERV_dup3481" "HERV_dup2896"
## [611] "HERV_dup1902" "HERV_dup572"  "HERV_dup1926" "HERV_dup3031" "HERV_dup3606"
## [616] "HERV_dup3117" "HERV_dup568"  "HERV_dup2809" "HERV_dup900"  "HERV_dup977" 
## [621] "HERV_dup1527" "HERV_dup2706" "HERV_dup1638" "HERV_dup1979" "HERV_dup924" 
## [626] "HERV_dup3212" "HERV_dup2482" "HERV_dup2404" "HERV_dup846"  "HERV_dup492" 
## [631] "HERV_dup1080" "HERV_dup1401" "HERV_dup86"   "HERV_dup39"   "HERV_dup3154"
## [636] "HERV_dup1823" "HERV_dup1228" "HERV_dup1556" "HERV_dup177"  "HERV_dup1195"
## [641] "HERV_dup2696" "HERV_dup78"   "HERV_dup2378" "HERV_dup2272" "HERV_dup3248"
## [646] "HERV_dup3215" "HERV_dup2945" "HERV_dup1327" "HERV_dup2977" "HERV_dup1103"
## [651] "HERV_dup2695" "HERV_dup3179" "HERV_dup399"  "HERV_dup1146" "HERV_dup1557"
## [656] "HERV_dup3319" "HERV_dup17"   "HERV_dup2149" "HERV_dup2479" "HERV_dup2464"
## [661] "HERV_dup1049" "HERV_dup3217" "HERV_dup1933" "HERV_dup133"  "HERV_dup1640"
## [666] "HERV_dup3588" "HERV_dup530"  "HERV_dup2942" "HERV_dup3131" "HERV_dup1254"
## [671] "HERV_dup595"  "HERV_dup3673" "HERV_dup1664" "HERV_dup1757" "HERV_dup2337"
## [676] "HERV_dup2620" "HERV_dup1962" "HERV_dup1673" "HERV_dup1868" "HERV_dup1639"
## [681] "HERV_dup277"  "HERV_dup982"  "HERV_dup3219" "HERV_dup201"  "HERV_dup3044"
## [686] "HERV_dup1943" "HERV_dup1013" "HERV_dup350"  "HERV_dup357"  "HERV_dup1218"
## [691] "HERV_dup2823" "HERV_dup2356" "HERV_dup3037" "HERV_dup2137" "HERV_dup1440"
## [696] "HERV_dup1346" "HERV_dup1944" "HERV_dup1182" "HERV_dup3328" "HERV_dup2978"
## [701] "HERV_dup3459" "HERV_dup1383" "HERV_dup1656" "HERV_dup739"  "HERV_dup1172"
## [706] "HERV_dup671"  "HERV_dup1532" "HERV_dup3196" "HERV_dup2730" "HERV_dup935" 
## [711] "HERV_dup2897" "HERV_dup2797" "HERV_dup1415" "HERV_dup1752" "HERV_dup2290"
## [716] "HERV_dup240"  "HERV_dup2159" "HERV_dup1520" "HERV_dup2680" "HERV_dup1364"
## [721] "HERV_dup2979" "HERV_dup930"  "HERV_dup2785" "HERV_dup591"  "HERV_dup2529"
## [726] "HERV_dup3607" "HERV_dup735"  "HERV_dup1099" "HERV_dup1549" "HERV_dup1711"
## [731] "HERV_dup3284" "HERV_dup3335" "HERV_dup336"  "HERV_dup3545" "HERV_dup3688"
## [736] "HERV_dup398"  "HERV_dup400"  "HERV_dup450"  "HERV_dup452"

8.2 Pseudobulk heatmaps clustering rows

• Heatmap visualization of expressed >6kbp L1HS-L1PA3 and HERVs on pseudobulks with more than 50 nuclei (line 318).
• Rows are clustered using a hierarchical clustering method within pheatmap.
• Excluded clusters 6 (VLMC) and 7 (Tcells) due to low number of nuclei.

I wanted to have the heatmaps of L1s and HERVs stacked but not mixed, so I’m collecting the order of the row clustering in a variable of shape heatmap_[region]_[TE]_order.

heatmap_pfc_L1 <- asap_heatmap_snRNA(region = c("PFC"), 
                   tes = data_TE_annotation[which(data_TE_annotation$type == "L1"),"TE_id"], 
                   return_df = F, 
                   breaks = seq(0,15,length.out = 52), 
                   group_rows = c("type"),
                   data = TE_data, group_cols = c("celltype"),
                   order_cols_groups = order_cols_celltype,
                   title = "PFC L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
                   exclude_clusters = c(6, 7))

heatmap_pfc_L1_order <- heatmap_pfc_L1$order_rows

heatmap_pfc_HERV <- asap_heatmap_snRNA(region = c("PFC"), 
                   tes = data_TE_annotation[which(data_TE_annotation$type == "HERV"),"TE_id"], 
                   return_df = F, 
                   group_rows = c("type"),
                   breaks = seq(0,15,length.out = 52), 
                   data = TE_data, group_cols = c("celltype"),
                   order_cols_groups = order_cols_celltype,
                   title = "PFC HERVs: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
                   exclude_clusters = c(6, 7))

heatmap_pfc_HERV_order <- heatmap_pfc_HERV$order_rows

heatmap_put_L1 <- asap_heatmap_snRNA(region = c("PUT"), 
                   tes = data_TE_annotation[which(data_TE_annotation$type == "L1"),"TE_id"], 
                   return_df = F, 
                   group_rows = c("type"),
                   breaks = seq(0,15,length.out = 52), 
                   data = TE_data, group_cols = c("celltype"),
                   order_cols_groups = order_cols_celltype,
                   title = "PUT L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
                   exclude_clusters = c(6, 7))

heatmap_put_L1_order <- heatmap_put_L1$order_rows

heatmap_put_HERV <- asap_heatmap_snRNA(region = c("PUT"), 
                   tes = data_TE_annotation[which(data_TE_annotation$type == "HERV"),"TE_id"], 
                   return_df = F, 
                   group_rows = c("type"),
                   breaks = seq(0,15,length.out = 52), 
                   data = TE_data, group_cols = c("celltype"),
                   order_cols_groups = order_cols_celltype,
                   title = "PUT HERVs: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
                   exclude_clusters = c(6, 7))

heatmap_put_HERV_order <- heatmap_put_HERV$order_rows

heatmap_sn_L1 <- asap_heatmap_snRNA(region = c("SN"), 
                   tes = data_TE_annotation[which(data_TE_annotation$type == "L1"),"TE_id"], 
                   return_df = F, 
                   group_rows = c("type"),
                   breaks = seq(0,15,length.out = 52), 
                   data = TE_data, group_cols = c("celltype"),
                   order_cols_groups = order_cols_celltype,
                   title = "SN L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
                   exclude_clusters = c(6, 7))

heatmap_sn_L1_order <- heatmap_sn_L1$order_rows

heatmap_sn_HERV <- asap_heatmap_snRNA(region = c("SN"), 
                   tes = data_TE_annotation[which(data_TE_annotation$type == "HERV"),"TE_id"], 
                   return_df = F, 
                   group_rows = c("type"),
                   breaks = seq(0,15,length.out = 52), 
                   data = TE_data, group_cols = c("celltype"),
                   order_cols_groups = order_cols_celltype,
                   title = "SN HERVs: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
                   exclude_clusters = c(6, 7))

heatmap_sn_HERV_order <- heatmap_sn_HERV$order_rows

heatmap_amy_L1 <- asap_heatmap_snRNA(region = c("AMY"), 
                   tes = data_TE_annotation[which(data_TE_annotation$type == "L1"),"TE_id"], 
                   return_df = F, 
                   group_rows = c("type"),
                   breaks = seq(0,15,length.out = 52), 
                   data = TE_data, group_cols = c("celltype"),
                   order_cols_groups = order_cols_celltype,
                   title = "AMY L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
                   exclude_clusters = c(6, 7))

heatmap_amy_L1_order <- heatmap_amy_L1$order_rows

heatmap_amy_HERV <- asap_heatmap_snRNA(region = c("AMY"), 
                   tes = data_TE_annotation[which(data_TE_annotation$type == "HERV"),"TE_id"], 
                   return_df = F, 
                   group_rows = c("type"),
                   breaks = seq(0,15,length.out = 52), 
                   data = TE_data, group_cols = c("celltype"),
                   order_cols_groups = order_cols_celltype,
                   title = "AMY HERVs: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
                   exclude_clusters = c(6, 7))

heatmap_amy_HERV_order <- heatmap_amy_HERV$order_rows

Figure stacked heatmaps

I’m using the variables heatmap_[region]_[TE]_order to stack the L1 and HERV heatmaps on top of each other. These are the heatmaps shown in figure 3.

asap_heatmap_snRNA(region = c("PFC"), 
                   tes = data_TE_annotation$TE_id, 
                   return_df = F, group_rows = c("type"), 
                   gaps_row = length(heatmap_pfc_HERV_order),
                   breaks = seq(0,15,length.out = 52), index_row_reorder = c(heatmap_pfc_HERV_order,heatmap_pfc_L1_order),
                   order_cols_groups = order_cols_celltype,
                   data = TE_data, group_cols = c("celltype"),
                   title = "PFC HERVs + L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
                   exclude_clusters = c(6, 7))

## $heatmap
## 
## $order_cols
##   [1] "DA813_ASAP17_PD_NP16-140_PFC_0"   "DA804_ASAP49_ctrl_NP18-159_PFC_0"
##   [3] "DA775_ASAP22_PD_NP16-269_PFC_0"   "AA_ASAP81_PD_NP21-208_PFC_0"     
##   [5] "AA_ASAP91_ctrl_NP17-20_PFC_0"     "AA_ASAP85_NP18-46_ctrl_PFC_0"    
##   [7] "MJ_ASAP14_ctrl_NP16-164_PFC_0"    "AA_ASAP151_PD_NP17-232_PFC_0"    
##   [9] "ASAP155_ctrl_NP23-21_PFC_0"       "AA_ASAP116_PD_NP22-55_PFC_0"     
##  [11] "AA_ASAP152_PD_NP19-91_PFC_0"      "AA_ASAP89_ctrl_NP16-284_PFC_0"   
##  [13] "AA_ASAP90_ctrl_NP16-293_PFC_0"    "AA_ASAP145_ctrl_NP19-218_PFC_0"  
##  [15] "DA480_ASAP15_ctrl_NP16-21_PFC_0"  "DA795_ASAP55_ctrl_NP19-37_PFC_0" 
##  [17] "DA476_ASAP10_PD_NP16-25_PFC_0"    "AA_ASAP82_PD_NP21-217_PFC_0"     
##  [19] "DA809_ASAP30_PD_NP18-117_PFC_0"   "DA777_ASAP28_PD_NP17-191_PFC_0"  
##  [21] "DA499_ASAP44_PD_NP19-255_PFC_0"   "AA_ASAP153_ctrl_NP19-137_PFC_0"  
##  [23] "DA432_ASAP12_PD_P74_PFC_0"        "DA806_ASAP58_ctrl_NP19-45_PFC_0" 
##  [25] "DA488_ASAP16_ctrl_PT231_PFC_0"    "DA428_ASAP13_ctrl_NP16-161_PFC_0"
##  [27] "DA810_ASAP34_PD_NP18-304_PFC_0"   "AA_ASAP83_NP16-119_ctrl_PFC_0"   
##  [29] "DA430_ASAP9_PD_NP16-162_PFC_0"    "DA509_ASAP36_PD_NP19-16_PFC_0"   
##  [31] "DA490_ASAP11_PD_P73_PFC_0"        "AA_ASAP80_PD_NP21-57_PFC_0"      
##  [33] "AA_ASAP86_NP18-148_ctrl_PFC_0"    "AA_ASAP90_ctrl_NP16-293_PFC_1"   
##  [35] "AA_ASAP89_ctrl_NP16-284_PFC_1"    "DA490_ASAP11_PD_P73_PFC_1"       
##  [37] "DA509_ASAP36_PD_NP19-16_PFC_1"    "ASAP155_ctrl_NP23-21_PFC_1"      
##  [39] "AA_ASAP116_PD_NP22-55_PFC_1"      "MJ_ASAP14_ctrl_NP16-164_PFC_1"   
##  [41] "AA_ASAP151_PD_NP17-232_PFC_1"     "DA795_ASAP55_ctrl_NP19-37_PFC_1" 
##  [43] "AA_ASAP153_ctrl_NP19-137_PFC_1"   "AA_ASAP91_ctrl_NP17-20_PFC_1"    
##  [45] "AA_ASAP85_NP18-46_ctrl_PFC_1"     "DA480_ASAP15_ctrl_NP16-21_PFC_1" 
##  [47] "AA_ASAP145_ctrl_NP19-218_PFC_1"   "AA_ASAP82_PD_NP21-217_PFC_1"     
##  [49] "AA_ASAP81_PD_NP21-208_PFC_1"      "DA777_ASAP28_PD_NP17-191_PFC_1"  
##  [51] "DA809_ASAP30_PD_NP18-117_PFC_1"   "AA_ASAP86_NP18-148_ctrl_PFC_1"   
##  [53] "AA_ASAP83_NP16-119_ctrl_PFC_1"    "DA430_ASAP9_PD_NP16-162_PFC_1"   
##  [55] "DA476_ASAP10_PD_NP16-25_PFC_1"    "DA488_ASAP16_ctrl_PT231_PFC_1"   
##  [57] "DA810_ASAP34_PD_NP18-304_PFC_1"   "DA806_ASAP58_ctrl_NP19-45_PFC_1" 
##  [59] "DA428_ASAP13_ctrl_NP16-161_PFC_1" "AA_ASAP152_PD_NP19-91_PFC_1"     
##  [61] "DA432_ASAP12_PD_P74_PFC_1"        "DA499_ASAP44_PD_NP19-255_PFC_1"  
##  [63] "AA_ASAP80_PD_NP21-57_PFC_1"       "DA804_ASAP49_ctrl_NP18-159_PFC_1"
##  [65] "DA775_ASAP22_PD_NP16-269_PFC_1"   "AA_ASAP150_PD_NP16-285_PFC_2"    
##  [67] "DA785_ASAP47_ctrl_NP17-256_PFC_2" "AA_ASAP81_PD_NP21-208_PFC_2"     
##  [69] "DA490_ASAP11_PD_P73_PFC_2"        "DA509_ASAP36_PD_NP19-16_PFC_2"   
##  [71] "DA432_ASAP12_PD_P74_PFC_2"        "AA_ASAP84_NP17-216_ctrl_PFC_2"   
##  [73] "AA_ASAP154_ctrl_NP21-04_PFC_2"    "AA_ASAP91_ctrl_NP17-20_PFC_2"    
##  [75] "AA_ASAP145_ctrl_NP19-218_PFC_2"   "DA795_ASAP55_ctrl_NP19-37_PFC_2" 
##  [77] "DA476_ASAP10_PD_NP16-25_PFC_2"    "AA_ASAP151_PD_NP17-232_PFC_2"    
##  [79] "DA430_ASAP9_PD_NP16-162_PFC_2"    "AA_ASAP83_NP16-119_ctrl_PFC_2"   
##  [81] "AA_ASAP80_PD_NP21-57_PFC_2"       "DA806_ASAP58_ctrl_NP19-45_PFC_2" 
##  [83] "DA810_ASAP34_PD_NP18-304_PFC_2"   "AA_ASAP116_PD_NP22-55_PFC_2"     
##  [85] "AA_ASAP89_ctrl_NP16-284_PFC_2"    "AA_ASAP86_NP18-148_ctrl_PFC_2"   
##  [87] "DA480_ASAP15_ctrl_NP16-21_PFC_2"  "MJ_ASAP14_ctrl_NP16-164_PFC_2"   
##  [89] "DA499_ASAP44_PD_NP19-255_PFC_2"   "DA428_ASAP13_ctrl_NP16-161_PFC_2"
##  [91] "AA_ASAP152_PD_NP19-91_PFC_2"      "DA488_ASAP16_ctrl_PT231_PFC_2"   
##  [93] "AA_ASAP90_ctrl_NP16-293_PFC_2"    "AA_ASAP82_PD_NP21-217_PFC_2"     
##  [95] "AA_ASAP153_ctrl_NP19-137_PFC_2"   "ASAP155_ctrl_NP23-21_PFC_2"      
##  [97] "DA808_ASAP41_PD_NP19-108_PFC_2"   "DA775_ASAP22_PD_NP16-269_PFC_2"  
##  [99] "DA809_ASAP30_PD_NP18-117_PFC_2"   "DA804_ASAP49_ctrl_NP18-159_PFC_2"
## [101] "AA_ASAP84_NP17-216_ctrl_PFC_3"    "AA_ASAP154_ctrl_NP21-04_PFC_3"   
## [103] "AA_ASAP91_ctrl_NP17-20_PFC_3"     "AA_ASAP150_PD_NP16-285_PFC_3"    
## [105] "AA_ASAP145_ctrl_NP19-218_PFC_3"   "DA432_ASAP12_PD_P74_PFC_3"       
## [107] "ASAP155_ctrl_NP23-21_PFC_3"       "AA_ASAP86_NP18-148_ctrl_PFC_3"   
## [109] "AA_ASAP152_PD_NP19-91_PFC_3"      "DA509_ASAP36_PD_NP19-16_PFC_3"   
## [111] "AA_ASAP90_ctrl_NP16-293_PFC_3"    "DA490_ASAP11_PD_P73_PFC_3"       
## [113] "DA775_ASAP22_PD_NP16-269_PFC_3"   "DA795_ASAP55_ctrl_NP19-37_PFC_3" 
## [115] "DA476_ASAP10_PD_NP16-25_PFC_3"    "DA804_ASAP49_ctrl_NP18-159_PFC_3"
## [117] "DA809_ASAP30_PD_NP18-117_PFC_3"   "DA430_ASAP9_PD_NP16-162_PFC_3"   
## [119] "DA810_ASAP34_PD_NP18-304_PFC_3"   "DA428_ASAP13_ctrl_NP16-161_PFC_3"
## [121] "DA488_ASAP16_ctrl_PT231_PFC_3"    "AA_ASAP80_PD_NP21-57_PFC_3"      
## [123] "DA806_ASAP58_ctrl_NP19-45_PFC_3"  "DA499_ASAP44_PD_NP19-255_PFC_3"  
## [125] "AA_ASAP83_NP16-119_ctrl_PFC_3"    "AA_ASAP82_PD_NP21-217_PFC_3"     
## [127] "DA480_ASAP15_ctrl_NP16-21_PFC_3"  "DA777_ASAP28_PD_NP17-191_PFC_3"  
## [129] "AA_ASAP89_ctrl_NP16-284_PFC_3"    "AA_ASAP151_PD_NP17-232_PFC_3"    
## [131] "AA_ASAP116_PD_NP22-55_PFC_3"      "MJ_ASAP14_ctrl_NP16-164_PFC_3"   
## [133] "DA785_ASAP47_ctrl_NP17-256_PFC_3" "DA785_ASAP47_ctrl_NP17-256_PFC_5"
## [135] "MJ_ASAP14_ctrl_NP16-164_PFC_5"    "ASAP155_ctrl_NP23-21_PFC_5"      
## [137] "AA_ASAP153_ctrl_NP19-137_PFC_5"   "AA_ASAP85_NP18-46_ctrl_PFC_5"    
## [139] "AA_ASAP91_ctrl_NP17-20_PFC_5"     "AA_ASAP83_NP16-119_ctrl_PFC_5"   
## [141] "DA428_ASAP13_ctrl_NP16-161_PFC_5" "AA_ASAP90_ctrl_NP16-293_PFC_5"   
## [143] "DA430_ASAP9_PD_NP16-162_PFC_5"    "AA_ASAP89_ctrl_NP16-284_PFC_5"   
## [145] "DA432_ASAP12_PD_P74_PFC_5"        "DA490_ASAP11_PD_P73_PFC_5"       
## [147] "DA509_ASAP36_PD_NP19-16_PFC_5"    "AA_ASAP84_NP17-216_ctrl_PFC_5"   
## [149] "AA_ASAP154_ctrl_NP21-04_PFC_5"    "DA799_ASAP19_PD_NP16-160_PFC_5"  
## [151] "DA813_ASAP17_PD_NP16-140_PFC_5"   "DA808_ASAP41_PD_NP19-108_PFC_5"  
## [153] "AA_ASAP150_PD_NP16-285_PFC_5"     "AA_ASAP151_PD_NP17-232_PFC_5"    
## [155] "DA809_ASAP30_PD_NP18-117_PFC_5"   "DA804_ASAP49_ctrl_NP18-159_PFC_5"
## [157] "DA476_ASAP10_PD_NP16-25_PFC_5"    "DA795_ASAP55_ctrl_NP19-37_PFC_5" 
## [159] "AA_ASAP116_PD_NP22-55_PFC_5"      "AA_ASAP147_ctrl_NP22-37_PFC_5"   
## [161] "DA775_ASAP22_PD_NP16-269_PFC_5"   "DA480_ASAP15_ctrl_NP16-21_PFC_5" 
## [163] "DA777_ASAP28_PD_NP17-191_PFC_5"   "DA806_ASAP58_ctrl_NP19-45_PFC_5" 
## [165] "AA_ASAP152_PD_NP19-91_PFC_5"      "AA_ASAP145_ctrl_NP19-218_PFC_5"  
## [167] "AA_ASAP86_NP18-148_ctrl_PFC_5"    "DA499_ASAP44_PD_NP19-255_PFC_5"  
## [169] "AA_ASAP82_PD_NP21-217_PFC_5"      "AA_ASAP80_PD_NP21-57_PFC_5"      
## [171] "DA488_ASAP16_ctrl_PT231_PFC_5"    "DA810_ASAP34_PD_NP18-304_PFC_5"  
## [173] "DA775_ASAP22_PD_NP16-269_PFC_4"   "AA_ASAP89_ctrl_NP16-284_PFC_4"   
## [175] "AA_ASAP90_ctrl_NP16-293_PFC_4"    "DA428_ASAP13_ctrl_NP16-161_PFC_4"
## [177] "DA488_ASAP16_ctrl_PT231_PFC_4"    "AA_ASAP80_PD_NP21-57_PFC_4"      
## [179] "AA_ASAP152_PD_NP19-91_PFC_4"      "AA_ASAP82_PD_NP21-217_PFC_4"     
## [181] "AA_ASAP151_PD_NP17-232_PFC_4"     "AA_ASAP83_NP16-119_ctrl_PFC_4"   
## [183] "DA806_ASAP58_ctrl_NP19-45_PFC_4"  "AA_ASAP145_ctrl_NP19-218_PFC_4"  
## [185] "AA_ASAP86_NP18-148_ctrl_PFC_4"    "DA480_ASAP15_ctrl_NP16-21_PFC_4" 
## [187] "DA432_ASAP12_PD_P74_PFC_4"        "MJ_ASAP14_ctrl_NP16-164_PFC_4"   
## [189] "ASAP155_ctrl_NP23-21_PFC_4"       "DA499_ASAP44_PD_NP19-255_PFC_4"  
## [191] "DA490_ASAP11_PD_P73_PFC_4"        "DA808_ASAP41_PD_NP19-108_PFC_4"  
## [193] "DA804_ASAP49_ctrl_NP18-159_PFC_4" "DA430_ASAP9_PD_NP16-162_PFC_4"   
## [195] "AA_ASAP116_PD_NP22-55_PFC_4"      "DA795_ASAP55_ctrl_NP19-37_PFC_4" 
## [197] "DA476_ASAP10_PD_NP16-25_PFC_4"   
## 
## $order_rows
##    [1] "HERV_dup3363"   "HERV_dup2977"   "HERV_dup2555"   "HERV_dup1948"  
##    [5] "HERV_dup2809"   "HERV_dup1556"   "HERV_dup1730"   "HERV_dup723"   
##    [9] "HERV_dup3227"   "HERV_dup551"    "HERV_dup2879"   "HERV_dup369"   
##   [13] "HERV_dup1303"   "HERV_dup1823"   "HERV_dup977"    "HERV_dup276"   
##   [17] "HERV_dup3189"   "HERV_dup2848"   "HERV_dup3507"   "HERV_dup3505"  
##   [21] "HERV_dup2847"   "HERV_dup2093"   "HERV_dup2743"   "HERV_dup2599"  
##   [25] "HERV_dup2772"   "HERV_dup3171"   "HERV_dup1272"   "HERV_dup851"   
##   [29] "HERV_dup348"    "HERV_dup2319"   "HERV_dup1321"   "HERV_dup916"   
##   [33] "HERV_dup1658"   "HERV_dup3196"   "HERV_dup1036"   "HERV_dup508"   
##   [37] "HERV_dup831"    "HERV_dup399"    "HERV_dup1208"   "HERV_dup1943"  
##   [41] "HERV_dup2320"   "HERV_dup243"    "HERV_dup631"    "HERV_dup565"   
##   [45] "HERV_dup336"    "HERV_dup1673"   "HERV_dup23"     "HERV_dup250"   
##   [49] "HERV_dup2730"   "HERV_dup251"    "HERV_dup2130"   "HERV_dup1520"  
##   [53] "HERV_dup968"    "HERV_dup2907"   "HERV_dup1605"   "HERV_dup3459"  
##   [57] "HERV_dup329"    "HERV_dup626"    "HERV_dup2566"   "HERV_dup640"   
##   [61] "HERV_dup2041"   "HERV_dup3694"   "HERV_dup2934"   "HERV_dup3117"  
##   [65] "HERV_dup3341"   "HERV_dup3328"   "HERV_dup2476"   "HERV_dup1324"  
##   [69] "HERV_dup934"    "HERV_dup2112"   "HERV_dup1447"   "HERV_dup1319"  
##   [73] "HERV_dup202"    "HERV_dup203"    "HERV_dup990"    "HERV_dup2292"  
##   [77] "HERV_dup218"    "HERV_dup2784"   "HERV_dup2366"   "HERV_dup1362"  
##   [81] "HERV_dup282"    "HERV_dup446"    "HERV_dup2941"   "HERV_dup2383"  
##   [85] "HERV_dup1657"   "HERV_dup2404"   "HERV_dup1891"   "HERV_dup1304"  
##   [89] "HERV_dup2152"   "HERV_dup1331"   "HERV_dup2939"   "HERV_dup1557"  
##   [93] "HERV_dup1089"   "HERV_dup2886"   "HERV_dup183"    "HERV_dup3044"  
##   [97] "HERV_dup2557"   "HERV_dup1003"   "HERV_dup1187"   "HERV_dup57"    
##  [101] "HERV_dup1302"   "HERV_dup2655"   "HERV_dup1933"   "HERV_dup1932"  
##  [105] "HERV_dup2479"   "HERV_dup1757"   "HERV_dup2187"   "HERV_dup2936"  
##  [109] "HERV_dup3284"   "HERV_dup595"    "HERV_dup1440"   "HERV_dup1049"  
##  [113] "HERV_dup133"    "HERV_dup471"    "HERV_dup1210"   "HERV_dup1093"  
##  [117] "HERV_dup2441"   "HERV_dup1438"   "HERV_dup398"    "HERV_dup400"   
##  [121] "HERV_dup1415"   "HERV_dup3182"   "HERV_dup441"    "HERV_dup982"   
##  [125] "HERV_dup1389"   "HERV_dup2635"   "HERV_dup2536"   "HERV_dup1228"  
##  [129] "HERV_dup2942"   "HERV_dup572"    "HERV_dup115"    "HERV_dup272"   
##  [133] "HERV_dup467"    "HERV_dup2647"   "HERV_dup194"    "HERV_dup1007"  
##  [137] "HERV_dup201"    "HERV_dup301"    "HERV_dup469"    "HERV_dup1366"  
##  [141] "HERV_dup732"    "HERV_dup3212"   "HERV_dup1245"   "HERV_dup2604"  
##  [145] "HERV_dup736"    "HERV_dup1099"   "HERV_dup729"    "HERV_dup1218"  
##  [149] "HERV_dup1108"   "HERV_dup728"    "HERV_dup935"    "HERV_dup2264"  
##  [153] "HERV_dup3154"   "HERV_dup1346"   "HERV_dup443"    "HERV_dup634"   
##  [157] "HERV_dup381"    "HERV_dup517"    "HERV_dup344"    "HERV_dup1514"  
##  [161] "HERV_dup1638"   "HERV_dup388"    "HERV_dup17"     "HERV_dup682"   
##  [165] "HERV_dup530"    "HERV_dup1937"   "HERV_dup509"    "HERV_dup2972"  
##  [169] "HERV_dup1146"   "HERV_dup2823"   "HERV_dup735"    "HERV_dup772"   
##  [173] "HERV_dup3215"   "HERV_dup2464"   "HERV_dup1131"   "HERV_dup568"   
##  [177] "HERV_dup1278"   "HERV_dup1668"   "HERV_dup1378"   "HERV_dup2129"  
##  [181] "HERV_dup2518"   "HERV_dup884"    "HERV_dup2481"   "HERV_dup1944"  
##  [185] "HERV_dup1494"   "HERV_dup2217"   "HERV_dup2602"   "HERV_dup1776"  
##  [189] "HERV_dup556"    "HERV_dup1254"   "HERV_dup1869"   "HERV_dup1931"  
##  [193] "HERV_dup3408"   "HERV_dup2324"   "HERV_dup3688"   "HERV_dup570"   
##  [197] "HERV_dup1724"   "HERV_dup1639"   "HERV_dup2272"   "HERV_dup554"   
##  [201] "HERV_dup184"    "HERV_dup3016"   "HERV_dup321"    "HERV_dup1112"  
##  [205] "HERV_dup3073"   "HERV_dup447"    "HERV_dup357"    "HERV_dup2034"  
##  [209] "HERV_dup1273"   "HERV_dup1073"   "HERV_dup930"    "HERV_dup739"   
##  [213] "HERV_dup3545"   "HERV_dup1213"   "HERV_dup1958"   "HERV_dup314"   
##  [217] "HERV_dup3607"   "HERV_dup461"    "HERV_dup519"    "HERV_dup29"    
##  [221] "HERV_dup3481"   "HERV_dup3131"   "HERV_dup2620"   "HERV_dup180"   
##  [225] "HERV_dup3137"   "HERV_dup2747"   "HERV_dup177"    "HERV_dup966"   
##  [229] "HERV_dup2141"   "HERV_dup3015"   "HERV_dup1239"   "HERV_dup967"   
##  [233] "HERV_dup39"     "HERV_dup850"    "HERV_dup1934"   "HERV_dup2945"  
##  [237] "HERV_dup86"     "HERV_dup1295"   "HERV_dup2290"   "HERV_dup2878"  
##  [241] "HERV_dup1902"   "HERV_dup2603"   "HERV_dup2482"   "HERV_dup2242"  
##  [245] "HERV_dup2706"   "HERV_dup1374"   "HERV_dup3108"   "HERV_dup1403"  
##  [249] "HERV_dup3219"   "HERV_dup2033"   "HERV_dup1212"   "HERV_dup2804"  
##  [253] "HERV_dup692"    "HERV_dup84"     "HERV_dup291"    "HERV_dup3063"  
##  [257] "HERV_dup3588"   "HERV_dup1279"   "HERV_dup1733"   "HERV_dup870"   
##  [261] "HERV_dup3037"   "HERV_dup127"    "HERV_dup894"    "HERV_dup3031"  
##  [265] "HERV_dup1656"   "HERV_dup355"    "HERV_dup2797"   "HERV_dup3430"  
##  [269] "HERV_dup662"    "HERV_dup3519"   "HERV_dup2561"   "HERV_dup3406"  
##  [273] "HERV_dup1979"   "HERV_dup1248"   "HERV_dup3013"   "HERV_dup120"   
##  [277] "HERV_dup1236"   "HERV_dup185"    "HERV_dup3319"   "HERV_dup1005"  
##  [281] "HERV_dup3008"   "HERV_dup2680"   "HERV_dup1555"   "HERV_dup591"   
##  [285] "HERV_dup2128"   "HERV_dup1513"   "HERV_dup1071"   "HERV_dup2356"  
##  [289] "HERV_dup108"    "HERV_dup58"     "HERV_dup3416"   "HERV_dup1017"  
##  [293] "HERV_dup1156"   "HERV_dup2529"   "HERV_dup1532"   "HERV_dup3210"  
##  [297] "HERV_dup2100"   "HERV_dup3673"   "HERV_dup2857"   "HERV_dup2949"  
##  [301] "HERV_dup924"    "HERV_dup1496"   "HERV_dup34"     "HERV_dup505"   
##  [305] "HERV_dup2337"   "HERV_dup1500"   "HERV_dup1047"   "HERV_dup1222"  
##  [309] "HERV_dup389"    "HERV_dup2840"   "HERV_dup1640"   "HERV_dup1541"  
##  [313] "HERV_dup1655"   "HERV_dup1316"   "HERV_dup2525"   "HERV_dup2278"  
##  [317] "HERV_dup1253"   "HERV_dup2801"   "HERV_dup277"    "HERV_dup2778"  
##  [321] "HERV_dup1491"   "HERV_dup21"     "HERV_dup2548"   "HERV_dup2696"  
##  [325] "HERV_dup1107"   "HERV_dup1470"   "HERV_dup1923"   "HERV_dup3187"  
##  [329] "HERV_dup1401"   "HERV_dup1322"   "HERV_dup1661"   "HERV_dup1201"  
##  [333] "HERV_dup1184"   "HERV_dup1935"   "HERV_dup409"    "HERV_dup2027"  
##  [337] "HERV_dup773"    "HERV_dup1052"   "HERV_dup975"    "HERV_dup488"   
##  [341] "HERV_dup2646"   "HERV_dup1611"   "HERV_dup1307"   "HERV_dup3358"  
##  [345] "HERV_dup2533"   "HERV_dup1240"   "HERV_dup1614"   "HERV_dup1339"  
##  [349] "HERV_dup632"    "HERV_dup1755"   "HERV_dup703"    "HERV_dup487"   
##  [353] "HERV_dup2334"   "HERV_dup2905"   "HERV_dup1720"   "HERV_dup2530"  
##  [357] "HERV_dup2562"   "HERV_dup882"    "HERV_dup2378"   "HERV_dup1364"  
##  [361] "HERV_dup3050"   "HERV_dup2480"   "HERV_dup1350"   "HERV_dup3286"  
##  [365] "HERV_dup1914"   "HERV_dup1804"   "HERV_dup933"    "HERV_dup5"     
##  [369] "HERV_dup1390"   "HERV_dup2891"   "HERV_dup3217"   "HERV_dup2159"  
##  [373] "HERV_dup2663"   "HERV_dup2653"   "HERV_dup3100"   "HERV_dup3394"  
##  [377] "HERV_dup2843"   "HERV_dup3270"   "HERV_dup433"    "HERV_dup599"   
##  [381] "HERV_dup1526"   "HERV_dup1972"   "HERV_dup419"    "HERV_dup1356"  
##  [385] "HERV_dup1653"   "HERV_dup1327"   "HERV_dup1920"   "HERV_dup3366"  
##  [389] "HERV_dup710"    "HERV_dup1459"   "HERV_dup746"    "HERV_dup981"   
##  [393] "HERV_dup1064"   "HERV_dup577"    "HERV_dup665"    "HERV_dup876"   
##  [397] "HERV_dup578"    "HERV_dup2415"   "HERV_dup1453"   "HERV_dup1103"  
##  [401] "HERV_dup2735"   "HERV_dup2728"   "HERV_dup586"    "HERV_dup1046"  
##  [405] "HERV_dup1412"   "HERV_dup1851"   "HERV_dup1629"   "HERV_dup2978"  
##  [409] "HERV_dup2979"   "HERV_dup452"    "HERV_dup450"    "HERV_dup2303"  
##  [413] "HERV_dup1383"   "HERV_dup1962"   "HERV_dup3181"   "HERV_dup3179"  
##  [417] "HERV_dup356"    "HERV_dup1269"   "HERV_dup27"     "HERV_dup2250"  
##  [421] "HERV_dup2632"   "HERV_dup1433"   "HERV_dup331"    "HERV_dup2897"  
##  [425] "HERV_dup3239"   "HERV_dup1926"   "HERV_dup3107"   "HERV_dup2937"  
##  [429] "HERV_dup1029"   "HERV_dup3140"   "HERV_dup1413"   "HERV_dup909"   
##  [433] "HERV_dup2785"   "HERV_dup1847"   "HERV_dup1846"   "HERV_dup2550"  
##  [437] "HERV_dup1587"   "HERV_dup1268"   "HERV_dup118"    "HERV_dup2967"  
##  [441] "HERV_dup776"    "HERV_dup803"    "HERV_dup2149"   "HERV_dup1752"  
##  [445] "HERV_dup724"    "HERV_dup3287"   "HERV_dup846"    "HERV_dup1090"  
##  [449] "HERV_dup129"    "HERV_dup407"    "HERV_dup293"    "HERV_dup1579"  
##  [453] "HERV_dup152"    "HERV_dup613"    "HERV_dup573"    "HERV_dup799"   
##  [457] "HERV_dup2365"   "HERV_dup562"    "HERV_dup1359"   "HERV_dup2900"  
##  [461] "HERV_dup1050"   "HERV_dup386"    "HERV_dup214"    "HERV_dup3231"  
##  [465] "HERV_dup899"    "HERV_dup1334"   "HERV_dup2182"   "HERV_dup2736"  
##  [469] "HERV_dup3148"   "HERV_dup1081"   "HERV_dup1082"   "HERV_dup1717"  
##  [473] "HERV_dup1285"   "HERV_dup112"    "HERV_dup2651"   "HERV_dup904"   
##  [477] "HERV_dup1282"   "HERV_dup3351"   "HERV_dup2963"   "HERV_dup1750"  
##  [481] "HERV_dup1731"   "HERV_dup54"     "HERV_dup758"    "HERV_dup2391"  
##  [485] "HERV_dup2166"   "HERV_dup1662"   "HERV_dup434"    "HERV_dup1719"  
##  [489] "HERV_dup900"    "HERV_dup3105"   "HERV_dup2985"   "HERV_dup1333"  
##  [493] "HERV_dup1114"   "HERV_dup2282"   "HERV_dup377"    "HERV_dup1394"  
##  [497] "HERV_dup2964"   "HERV_dup890"    "HERV_dup2855"   "HERV_dup1351"  
##  [501] "HERV_dup2500"   "HERV_dup852"    "HERV_dup3124"   "HERV_dup1868"  
##  [505] "HERV_dup3522"   "HERV_dup1345"   "HERV_dup110"    "HERV_dup38"    
##  [509] "HERV_dup2436"   "HERV_dup873"    "HERV_dup1707"   "HERV_dup1381"  
##  [513] "HERV_dup1048"   "HERV_dup300"    "HERV_dup1080"   "HERV_dup2962"  
##  [517] "HERV_dup1780"   "HERV_dup3220"   "HERV_dup151"    "HERV_dup1890"  
##  [521] "HERV_dup2179"   "HERV_dup1953"   "HERV_dup1235"   "HERV_dup956"   
##  [525] "HERV_dup597"    "HERV_dup2631"   "HERV_dup2163"   "HERV_dup1778"  
##  [529] "HERV_dup18"     "HERV_dup2739"   "HERV_dup2607"   "HERV_dup1598"  
##  [533] "HERV_dup1437"   "HERV_dup880"    "HERV_dup290"    "HERV_dup2623"  
##  [537] "HERV_dup1940"   "HERV_dup2803"   "HERV_dup2643"   "HERV_dup3033"  
##  [541] "HERV_dup2733"   "HERV_dup1243"   "HERV_dup94"     "HERV_dup980"   
##  [545] "HERV_dup1298"   "HERV_dup1001"   "HERV_dup26"     "HERV_dup1371"  
##  [549] "HERV_dup1242"   "HERV_dup1663"   "HERV_dup2769"   "HERV_dup93"    
##  [553] "HERV_dup2589"   "HERV_dup2588"   "HERV_dup2896"   "HERV_dup1416"  
##  [557] "HERV_dup1875"   "HERV_dup1613"   "HERV_dup1195"   "HERV_dup350"   
##  [561] "HERV_dup2422"   "HERV_dup3335"   "HERV_dup492"    "HERV_dup215"   
##  [565] "HERV_dup3143"   "HERV_dup2188"   "HERV_dup2183"   "HERV_dup380"   
##  [569] "HERV_dup2273"   "HERV_dup2812"   "HERV_dup36"     "HERV_dup417"   
##  [573] "HERV_dup1417"   "HERV_dup2598"   "HERV_dup777"    "HERV_dup2299"  
##  [577] "HERV_dup2298"   "HERV_dup1703"   "HERV_dup2379"   "HERV_dup2834"  
##  [581] "HERV_dup2002"   "HERV_dup1512"   "HERV_dup3251"   "HERV_dup1617"  
##  [585] "HERV_dup2353"   "HERV_dup3198"   "HERV_dup2235"   "HERV_dup1569"  
##  [589] "HERV_dup2012"   "HERV_dup949"    "HERV_dup3410"   "HERV_dup2856"  
##  [593] "HERV_dup249"    "HERV_dup1209"   "HERV_dup2966"   "HERV_dup1281"  
##  [597] "HERV_dup1888"   "HERV_dup2019"   "HERV_dup2877"   "HERV_dup1671"  
##  [601] "HERV_dup1317"   "HERV_dup3365"   "HERV_dup671"    "HERV_dup670"   
##  [605] "HERV_dup2524"   "HERV_dup65"     "HERV_dup3118"   "HERV_dup3355"  
##  [609] "HERV_dup3529"   "HERV_dup3580"   "HERV_dup1982"   "HERV_dup2106"  
##  [613] "HERV_dup2176"   "HERV_dup1357"   "HERV_dup2085"   "HERV_dup1484"  
##  [617] "HERV_dup3266"   "HERV_dup1203"   "HERV_dup1694"   "HERV_dup1004"  
##  [621] "HERV_dup1102"   "HERV_dup1232"   "HERV_dup612"    "HERV_dup1756"  
##  [625] "HERV_dup2915"   "HERV_dup1382"   "HERV_dup939"    "HERV_dup2261"  
##  [629] "HERV_dup3418"   "HERV_dup2695"   "HERV_dup1702"   "HERV_dup872"   
##  [633] "HERV_dup2438"   "HERV_dup482"    "HERV_dup1315"   "HERV_dup2111"  
##  [637] "HERV_dup1596"   "HERV_dup1802"   "HERV_dup61"     "HERV_dup265"   
##  [641] "HERV_dup3342"   "HERV_dup3343"   "HERV_dup600"    "HERV_dup954"   
##  [645] "HERV_dup2914"   "HERV_dup2961"   "HERV_dup2412"   "HERV_dup1002"  
##  [649] "HERV_dup1283"   "HERV_dup1973"   "HERV_dup927"    "HERV_dup1297"  
##  [653] "HERV_dup1308"   "HERV_dup3390"   "HERV_dup1889"   "HERV_dup1358"  
##  [657] "HERV_dup2134"   "HERV_dup2789"   "HERV_dup292"    "HERV_dup1"     
##  [661] "HERV_dup1456"   "HERV_dup2376"   "HERV_dup474"    "HERV_dup2902"  
##  [665] "HERV_dup468"    "HERV_dup470"    "HERV_dup3226"   "HERV_dup1309"  
##  [669] "HERV_dup926"    "HERV_dup1255"   "HERV_dup209"    "HERV_dup913"   
##  [673] "HERV_dup1917"   "HERV_dup979"    "HERV_dup1749"   "HERV_dup3375"  
##  [677] "HERV_dup302"    "HERV_dup1000"   "HERV_dup1669"   "HERV_dup2841"  
##  [681] "HERV_dup288"    "HERV_dup717"    "HERV_dup731"    "HERV_dup3423"  
##  [685] "HERV_dup2491"   "HERV_dup1310"   "HERV_dup3174"   "HERV_dup2662"  
##  [689] "HERV_dup2752"   "HERV_dup3417"   "HERV_dup3388"   "HERV_dup2266"  
##  [693] "HERV_dup1670"   "HERV_dup37"     "HERV_dup384"    "HERV_dup2158"  
##  [697] "HERV_dup3379"   "HERV_dup518"    "HERV_dup969"    "HERV_dup3020"  
##  [701] "HERV_dup1449"   "HERV_dup1708"   "HERV_dup1079"   "HERV_dup1701"  
##  [705] "HERV_dup1758"   "HERV_dup2381"   "HERV_dup3252"   "HERV_dup3357"  
##  [709] "HERV_dup379"    "HERV_dup2880"   "HERV_dup2838"   "HERV_dup940"   
##  [713] "HERV_dup614"    "L1PA3_dup1010"  "L1PA3_dup4994"  "L1PA3_dup1311" 
##  [717] "L1PA3_dup2919"  "L1PA3_dup2517"  "L1PA3_dup8663"  "L1PA2_dup1272" 
##  [721] "L1PA3_dup4888"  "L1PA2_dup927"   "L1PA2_dup2245"  "L1PA3_dup1756" 
##  [725] "L1PA2_dup922"   "L1PA3_dup2593"  "L1PA2_dup1230"  "L1PA3_dup373"  
##  [729] "L1PA3_dup529"   "L1HS_dup455"    "L1PA2_dup410"   "L1PA3_dup527"  
##  [733] "L1PA3_dup2557"  "L1PA3_dup4277"  "L1PA3_dup6457"  "L1PA2_dup848"  
##  [737] "L1PA3_dup10686" "L1PA3_dup8903"  "L1PA3_dup4118"  "L1PA3_dup1651" 
##  [741] "L1PA3_dup1"     "L1PA2_dup196"   "L1HS_dup240"    "L1PA3_dup7862" 
##  [745] "L1PA3_dup10297" "L1PA2_dup3771"  "L1PA2_dup4403"  "L1PA3_dup10740"
##  [749] "L1HS_dup1462"   "L1PA2_dup4620"  "L1PA3_dup4349"  "L1PA2_dup2271" 
##  [753] "L1PA3_dup10011" "L1PA3_dup10096" "L1PA2_dup4612"  "L1PA2_dup1177" 
##  [757] "L1PA2_dup98"    "L1PA3_dup1647"  "L1PA2_dup1968"  "L1HS_dup1478"  
##  [761] "L1PA3_dup5106"  "L1PA3_dup3005"  "L1PA2_dup684"   "L1PA3_dup8313" 
##  [765] "L1PA2_dup2295"  "L1HS_dup811"    "L1PA3_dup7947"  "L1PA2_dup2047" 
##  [769] "L1PA3_dup10525" "L1HS_dup907"    "L1PA3_dup5594"  "L1HS_dup743"   
##  [773] "L1PA3_dup4259"  "L1PA2_dup4421"  "L1PA2_dup1023"  "L1PA2_dup16"   
##  [777] "L1PA3_dup6112"  "L1PA3_dup1463"  "L1PA2_dup4936"  "L1PA3_dup6884" 
##  [781] "L1PA3_dup8896"  "L1PA3_dup5358"  "L1PA3_dup5355"  "L1PA3_dup3763" 
##  [785] "L1PA3_dup7840"  "L1PA2_dup1621"  "L1PA2_dup423"   "L1PA3_dup3950" 
##  [789] "L1PA2_dup4043"  "L1PA3_dup2683"  "L1PA3_dup7432"  "L1HS_dup1576"  
##  [793] "L1PA2_dup949"   "L1PA2_dup1978"  "L1PA3_dup345"   "L1PA2_dup2581" 
##  [797] "L1PA2_dup1331"  "L1PA2_dup3003"  "L1HS_dup1324"   "L1PA3_dup6160" 
##  [801] "L1PA2_dup3930"  "L1PA2_dup4309"  "L1PA3_dup6008"  "L1PA3_dup9202" 
##  [805] "L1PA3_dup9856"  "L1PA3_dup3404"  "L1PA3_dup2643"  "L1PA3_dup3484" 
##  [809] "L1PA3_dup4393"  "L1PA2_dup4226"  "L1PA2_dup678"   "L1PA3_dup1328" 
##  [813] "L1HS_dup879"    "L1PA2_dup3283"  "L1PA3_dup7316"  "L1PA3_dup1026" 
##  [817] "L1PA3_dup1027"  "L1PA3_dup7605"  "L1PA3_dup5544"  "L1HS_dup1357"  
##  [821] "L1PA2_dup4262"  "L1PA3_dup400"   "L1PA2_dup2408"  "L1PA2_dup4776" 
##  [825] "L1PA3_dup9722"  "L1PA3_dup1337"  "L1PA2_dup1653"  "L1PA2_dup4045" 
##  [829] "L1PA2_dup805"   "L1HS_dup1019"   "L1PA3_dup1264"  "L1PA2_dup3881" 
##  [833] "L1PA3_dup9255"  "L1PA2_dup3607"  "L1PA3_dup9473"  "L1PA2_dup3405" 
##  [837] "L1PA3_dup4688"  "L1PA2_dup1770"  "L1PA2_dup4714"  "L1PA2_dup4440" 
##  [841] "L1PA2_dup2969"  "L1PA2_dup3622"  "L1PA2_dup2343"  "L1PA3_dup5418" 
##  [845] "L1PA2_dup1058"  "L1PA3_dup2755"  "L1PA2_dup4441"  "L1PA2_dup1375" 
##  [849] "L1HS_dup62"     "L1PA2_dup358"   "L1PA3_dup10176" "L1HS_dup1005"  
##  [853] "L1HS_dup995"    "L1PA2_dup4901"  "L1PA2_dup4618"  "L1PA2_dup4237" 
##  [857] "L1HS_dup1104"   "L1PA3_dup6387"  "L1PA2_dup747"   "L1PA2_dup4688" 
##  [861] "L1HS_dup35"     "L1HS_dup1286"   "L1PA2_dup1248"  "L1PA2_dup3503" 
##  [865] "L1PA2_dup514"   "L1PA3_dup6436"  "L1PA2_dup365"   "L1HS_dup679"   
##  [869] "L1PA3_dup5207"  "L1PA3_dup5928"  "L1PA3_dup1114"  "L1PA2_dup1112" 
##  [873] "L1PA2_dup2577"  "L1PA2_dup4454"  "L1PA3_dup10531" "L1PA3_dup8506" 
##  [877] "L1PA3_dup8117"  "L1PA2_dup4335"  "L1PA2_dup1463"  "L1PA2_dup1476" 
##  [881] "L1HS_dup143"    "L1HS_dup225"    "L1PA2_dup383"   "L1PA2_dup4686" 
##  [885] "L1PA2_dup1078"  "L1PA2_dup3445"  "L1PA2_dup2089"  "L1PA3_dup5866" 
##  [889] "L1PA2_dup1426"  "L1PA3_dup10043" "L1HS_dup600"    "L1HS_dup579"   
##  [893] "L1HS_dup1393"   "L1PA2_dup2180"  "L1PA2_dup4389"  "L1PA2_dup1490" 
##  [897] "L1PA2_dup2004"  "L1PA2_dup732"   "L1HS_dup1077"   "L1PA3_dup3291" 
##  [901] "L1PA2_dup935"   "L1HS_dup1243"   "L1HS_dup649"    "L1PA2_dup4762" 
##  [905] "L1HS_dup270"    "L1PA3_dup1279"  "L1PA3_dup2389"  "L1PA3_dup5057" 
##  [909] "L1HS_dup622"    "L1PA3_dup3153"  "L1PA3_dup6871"  "L1HS_dup1020"  
##  [913] "L1PA2_dup2506"  "L1PA2_dup4201"  "L1PA2_dup2261"  "L1PA2_dup2565" 
##  [917] "L1PA3_dup9702"  "L1HS_dup244"    "L1PA2_dup759"   "L1PA2_dup3776" 
##  [921] "L1PA3_dup1046"  "L1HS_dup111"    "L1PA2_dup4528"  "L1PA3_dup5886" 
##  [925] "L1PA2_dup4196"  "L1PA2_dup4639"  "L1PA2_dup2504"  "L1HS_dup1514"  
##  [929] "L1PA3_dup247"   "L1HS_dup787"    "L1HS_dup163"    "L1PA3_dup5363" 
##  [933] "L1PA3_dup638"   "L1PA2_dup109"   "L1PA2_dup4430"  "L1PA2_dup798"  
##  [937] "L1PA3_dup2620"  "L1HS_dup803"    "L1HS_dup87"     "L1HS_dup1339"  
##  [941] "L1PA3_dup3684"  "L1PA2_dup4548"  "L1PA3_dup8891"  "L1PA2_dup1398" 
##  [945] "L1PA2_dup3766"  "L1PA2_dup3160"  "L1HS_dup1014"   "L1PA2_dup2876" 
##  [949] "L1PA3_dup9866"  "L1HS_dup1437"   "L1PA3_dup5825"  "L1HS_dup376"   
##  [953] "L1PA2_dup4791"  "L1PA2_dup2127"  "L1HS_dup1501"   "L1PA3_dup1727" 
##  [957] "L1PA2_dup3426"  "L1HS_dup444"    "L1PA2_dup589"   "L1PA2_dup4432" 
##  [961] "L1PA2_dup2537"  "L1PA3_dup5540"  "L1PA3_dup6692"  "L1PA2_dup4522" 
##  [965] "L1PA2_dup4713"  "L1PA2_dup4478"  "L1PA3_dup7288"  "L1PA2_dup4611" 
##  [969] "L1HS_dup370"    "L1HS_dup1342"   "L1PA2_dup472"   "L1PA2_dup2444" 
##  [973] "L1PA3_dup840"   "L1PA2_dup4652"  "L1PA3_dup4687"  "L1HS_dup429"   
##  [977] "L1HS_dup466"    "L1HS_dup1284"   "L1PA2_dup726"   "L1PA3_dup683"  
##  [981] "L1PA3_dup1943"  "L1PA3_dup3959"  "L1HS_dup1616"   "L1PA2_dup2436" 
##  [985] "L1HS_dup802"    "L1PA2_dup382"   "L1HS_dup1491"   "L1PA2_dup3118" 
##  [989] "L1PA2_dup1049"  "L1HS_dup204"    "L1PA3_dup6523"  "L1PA2_dup1992" 
##  [993] "L1HS_dup1473"   "L1PA2_dup3439"  "L1PA2_dup3629"  "L1PA2_dup307"  
##  [997] "L1PA2_dup629"   "L1PA3_dup5927"  "L1PA2_dup4378"  "L1PA3_dup1989" 
## [1001] "L1PA2_dup360"   "L1PA3_dup7893"  "L1PA2_dup2168"  "L1PA2_dup2282" 
## [1005] "L1PA2_dup219"   "L1PA3_dup9840"  "L1PA2_dup1050"  "L1HS_dup90"    
## [1009] "L1PA2_dup2729"  "L1PA3_dup3586"  "L1HS_dup1295"   "L1PA2_dup71"   
## [1013] "L1PA3_dup165"   "L1PA2_dup142"   "L1PA3_dup5238"  "L1PA2_dup413"  
## [1017] "L1PA3_dup978"   "L1PA2_dup1933"  "L1PA3_dup2357"  "L1PA3_dup3954" 
## [1021] "L1PA3_dup6317"  "L1PA3_dup358"   "L1PA3_dup1547"  "L1PA2_dup2155" 
## [1025] "L1PA3_dup1269"  "L1PA3_dup7550"  "L1PA3_dup5534"  "L1PA2_dup1953" 
## [1029] "L1PA3_dup3968"  "L1PA2_dup1805"  "L1PA2_dup4030"  "L1PA3_dup8310" 
## [1033] "L1PA3_dup4708"  "L1PA3_dup9256"  "L1PA2_dup663"   "L1PA2_dup526"  
## [1037] "L1PA2_dup1418"  "L1PA3_dup4709"  "L1PA3_dup1800"  "L1PA2_dup1778" 
## [1041] "L1PA3_dup5514"  "L1PA3_dup5121"  "L1PA3_dup3758"  "L1PA3_dup3757" 
## [1045] "L1PA2_dup2289"  "L1PA3_dup4902"  "L1PA3_dup1723"  "L1HS_dup632"   
## [1049] "L1HS_dup1536"   "L1PA3_dup3306"  "L1PA2_dup3742"  "L1PA3_dup1952" 
## [1053] "L1HS_dup155"    "L1HS_dup948"    "L1PA3_dup5047"  "L1PA2_dup39"   
## [1057] "L1PA3_dup3300"  "L1PA2_dup1760"  "L1PA3_dup3880"  "L1PA3_dup4408" 
## [1061] "L1HS_dup596"    "L1PA3_dup5745"  "L1PA2_dup3042"  "L1PA3_dup6730" 
## [1065] "L1PA2_dup737"   "L1PA2_dup741"   "L1PA3_dup4596"  "L1PA2_dup595"  
## [1069] "L1PA3_dup2662"  "L1PA2_dup2496"  "L1PA2_dup4053"  "L1PA3_dup9373" 
## [1073] "L1PA2_dup675"   "L1PA3_dup9734"  "L1HS_dup1182"   "L1PA3_dup6929" 
## [1077] "L1PA3_dup10072" "L1PA2_dup3425"  "L1PA3_dup3729"  "L1PA3_dup3323" 
## [1081] "L1PA3_dup9946"  "L1PA3_dup3102"  "L1PA2_dup2385"  "L1PA3_dup4603" 
## [1085] "L1PA3_dup2204"  "L1PA3_dup8520"  "L1PA3_dup8872"  "L1PA3_dup3863" 
## [1089] "L1HS_dup449"    "L1PA3_dup1428"  "L1PA3_dup5510"  "L1PA3_dup8420" 
## [1093] "L1PA2_dup3773"  "L1PA2_dup4074"  "L1PA3_dup1770"  "L1HS_dup124"   
## [1097] "L1PA2_dup1560"  "L1PA3_dup8173"  "L1PA2_dup585"   "L1PA2_dup2680" 
## [1101] "L1PA3_dup2760"  "L1PA2_dup2720"  "L1PA2_dup662"   "L1PA2_dup4596" 
## [1105] "L1PA3_dup4487"  "L1PA3_dup9430"  "L1PA3_dup1988"  "L1PA3_dup8571" 
## [1109] "L1PA3_dup3307"  "L1PA2_dup4838"  "L1PA2_dup513"   "L1PA3_dup2721" 
## [1113] "L1PA3_dup6147"  "L1PA3_dup6573"  "L1PA2_dup4775"  "L1HS_dup916"   
## [1117] "L1PA3_dup6584"  "L1PA3_dup2954"  "L1PA2_dup1749"  "L1PA3_dup4804" 
## [1121] "L1PA3_dup4884"  "L1PA3_dup4885"  "L1PA3_dup872"   "L1PA3_dup2039" 
## [1125] "L1PA3_dup761"   "L1PA3_dup7237"  "L1PA3_dup4391"  "L1PA2_dup3805" 
## [1129] "L1PA2_dup3589"  "L1PA3_dup3507"  "L1PA2_dup200"   "L1PA3_dup3168" 
## [1133] "L1PA3_dup7821"  "L1PA3_dup1710"  "L1PA2_dup1298"  "L1PA3_dup7472" 
## [1137] "L1PA3_dup4891"  "L1PA3_dup7963"  "L1PA3_dup4401"  "L1PA3_dup7951" 
## [1141] "L1PA2_dup3736"  "L1PA2_dup2909"  "L1HS_dup1330"   "L1PA3_dup6002" 
## [1145] "L1PA2_dup221"   "L1PA3_dup10285" "L1PA3_dup3941"  "L1PA2_dup635"  
## [1149] "L1PA3_dup6385"  "L1PA3_dup2272"  "L1HS_dup191"    "L1PA2_dup1752" 
## [1153] "L1PA2_dup559"   "L1PA2_dup2860"  "L1HS_dup514"    "L1PA3_dup6434" 
## [1157] "L1PA3_dup9280"  "L1PA3_dup561"   "L1PA2_dup2164"  "L1HS_dup788"   
## [1161] "L1PA2_dup1462"  "L1PA2_dup1379"  "L1PA3_dup5680"  "L1PA2_dup791"  
## [1165] "L1PA3_dup10119" "L1PA3_dup8525"  "L1PA2_dup2988"  "L1PA3_dup7864" 
## [1169] "L1HS_dup138"    "L1PA3_dup7470"  "L1PA2_dup3531"  "L1PA2_dup234"  
## [1173] "L1PA3_dup8007"  "L1PA3_dup9998"  "L1PA2_dup130"   "L1PA3_dup5337" 
## [1177] "L1HS_dup831"    "L1PA3_dup1528"  "L1PA3_dup10344" "L1PA3_dup8522" 
## [1181] "L1PA2_dup3292"  "L1PA2_dup3615"  "L1HS_dup379"    "L1PA2_dup4651" 
## [1185] "L1PA3_dup8328"  "L1PA3_dup6966"  "L1PA3_dup3502"  "L1PA2_dup1746" 
## [1189] "L1PA3_dup6347"  "L1PA2_dup3136"  "L1HS_dup405"    "L1PA2_dup2863" 
## [1193] "L1PA3_dup1554"  "L1PA2_dup326"   "L1PA3_dup3509"  "L1PA2_dup994"  
## [1197] "L1PA2_dup2430"  "L1PA3_dup5468"  "L1PA2_dup2254"  "L1PA2_dup3484" 
## [1201] "L1PA2_dup727"   "L1PA2_dup3579"  "L1PA3_dup1550"  "L1PA3_dup4668" 
## [1205] "L1PA3_dup7792"  "L1PA3_dup2393"  "L1PA2_dup3437"  "L1PA3_dup9095" 
## [1209] "L1PA3_dup1937"  "L1PA2_dup4367"  "L1PA3_dup128"   "L1PA3_dup124"  
## [1213] "L1PA2_dup2791"  "L1PA3_dup7637"  "L1PA3_dup4122"  "L1PA3_dup907"  
## [1217] "L1HS_dup337"    "L1PA3_dup6036"  "L1PA2_dup4905"  "L1PA3_dup2551" 
## [1221] "L1PA2_dup2091"  "L1PA3_dup398"   "L1PA2_dup378"   "L1PA2_dup530"  
## [1225] "L1PA3_dup2744"  "L1PA3_dup9021"  "L1PA2_dup3664"  "L1PA2_dup37"   
## [1229] "L1HS_dup800"    "L1PA3_dup6550"  "L1PA3_dup748"   "L1PA3_dup4492" 
## [1233] "L1PA3_dup2413"

asap_heatmap_snRNA(region = c("PUT"), 
                   tes = data_TE_annotation$TE_id, 
                   return_df = F, group_rows = c("type"), gaps_row = length(heatmap_put_HERV_order),
                   breaks = seq(0,15,length.out = 52), index_row_reorder = c(heatmap_put_HERV_order,heatmap_put_L1_order),
                   order_cols_groups = order_cols_celltype,
                   data = TE_data, group_cols = c("celltype"),
                   title = "PUT HERVs + L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
                   exclude_clusters = c(6, 7))

## $heatmap
## 
## $order_cols
##   [1] "AA82_ASAP68_PD_NP18-117_PUT_0"   "AA_ASAP98_ctrl_NP16-119_PUT_0"  
##   [3] "AA_ASAP138_PD_NP16-285_PUT_0"    "AA79_ASAP64_PD_NP16-162_PUT_0"  
##   [5] "AA71_ASAP70_PD_NP18-304_PUT_0"   "AA_ASAP141_ctrl_NP19-218_PUT_0" 
##   [7] "AA_ASAP97_PD_NP21-57_PUT_0"      "AA_ASAP100_ctrl_NP18-148_PUT_0" 
##   [9] "AA84_ASAP71_PD_NP19-16_PUT_0"    "AA87_ASAP76_ctrl_NP18-159_PUT_0"
##  [11] "AA74_ASAP62_PD_NP16-140_PUT_0"   "AA84_ASAP71_PD_NP19-16_PUT_1"   
##  [13] "AA71_ASAP70_PD_NP18-304_PUT_1"   "AA_ASAP100_ctrl_NP18-148_PUT_1" 
##  [15] "AA79_ASAP64_PD_NP16-162_PUT_1"   "AA87_ASAP76_ctrl_NP18-159_PUT_1"
##  [17] "AA74_ASAP62_PD_NP16-140_PUT_1"   "AA_ASAP139_PD_NP17-232_PUT_1"   
##  [19] "AA_ASAP144_PD_NP19-137_PUT_1"    "AA_ASAP92_ctrl_NP16-284_PUT_1"  
##  [21] "AA_ASAP117_PD_NP22-55_PUT_1"     "AA_ASAP87_PD_NP21-208_PUT_1"    
##  [23] "AA_ASAP88_PD_NP21-217_PUT_1"     "AA_ASAP88_PD_NP21-217_PUT_2"    
##  [25] "AA85_ASAP72_PD_NP19-23_PUT_2"    "AA73_ASAP65_PD_NP16-269_PUT_2"  
##  [27] "AA82_ASAP68_PD_NP18-117_PUT_2"   "AA86_ASAP73_PD_NP19-108_PUT_2"  
##  [29] "AA_ASAP144_PD_NP19-137_PUT_2"    "AA79_ASAP64_PD_NP16-162_PUT_2"  
##  [31] "AA_ASAP117_PD_NP22-55_PUT_2"     "AA83_ASAP69_PD_NP18-287_PUT_2"  
##  [33] "AA81_ASAP67_PD_NP17-191_PUT_2"   "AA77_ASAP61_PD_NP16-25_PUT_2"   
##  [35] "AA_ASAP140_PD_NP19-91_PUT_2"     "AA_ASAP141_ctrl_NP19-218_PUT_2" 
##  [37] "AA76_ASAP74_PD_NP19-255_PUT_2"   "AA_ASAP96_ctrl_NP18-46_PUT_2"   
##  [39] "AA88_ASAP77_ctrl_NP19-36_PUT_2"  "AA89_ASAP78_ctrl_NP19-37_PUT_2" 
##  [41] "AA_ASAP94_ctrl_NP17-20_PUT_2"    "AA_ASAP139_PD_NP17-232_PUT_2"   
##  [43] "AA_ASAP93_ctrl_NP16-293_PUT_2"   "AA71_ASAP70_PD_NP18-304_PUT_2"  
##  [45] "AA74_ASAP62_PD_NP16-140_PUT_2"   "AA_ASAP87_PD_NP21-208_PUT_2"    
##  [47] "AA_ASAP97_PD_NP21-57_PUT_2"      "AA84_ASAP71_PD_NP19-16_PUT_2"   
##  [49] "AA87_ASAP76_ctrl_NP18-159_PUT_2" "AA_ASAP100_ctrl_NP18-148_PUT_2" 
##  [51] "AA_ASAP138_PD_NP16-285_PUT_2"    "AA_ASAP98_ctrl_NP16-119_PUT_2"  
##  [53] "AA_ASAP92_ctrl_NP16-284_PUT_2"   "AA_ASAP146_PD_NP21-04_PUT_2"    
##  [55] "AA_ASAP139_PD_NP17-232_PUT_3"    "AA_ASAP117_PD_NP22-55_PUT_3"    
##  [57] "AA_ASAP138_PD_NP16-285_PUT_3"    "AA79_ASAP64_PD_NP16-162_PUT_3"  
##  [59] "AA_ASAP100_ctrl_NP18-148_PUT_3"  "AA_ASAP141_ctrl_NP19-218_PUT_3" 
##  [61] "AA_ASAP144_PD_NP19-137_PUT_3"    "AA84_ASAP71_PD_NP19-16_PUT_3"   
##  [63] "AA_ASAP97_PD_NP21-57_PUT_3"      "AA87_ASAP76_ctrl_NP18-159_PUT_3"
##  [65] "AA85_ASAP72_PD_NP19-23_PUT_3"    "AA88_ASAP77_ctrl_NP19-36_PUT_3" 
##  [67] "AA_ASAP140_PD_NP19-91_PUT_3"     "AA_ASAP142_ctrl_NP22-37_PUT_3"  
##  [69] "AA86_ASAP73_PD_NP19-108_PUT_3"   "AA74_ASAP62_PD_NP16-140_PUT_3"  
##  [71] "AA_ASAP93_ctrl_NP16-293_PUT_3"   "AA_ASAP149_PD_NP23-21_PUT_3"    
##  [73] "AA89_ASAP78_ctrl_NP19-37_PUT_3"  "AA_ASAP146_PD_NP21-04_PUT_3"    
##  [75] "AA76_ASAP74_PD_NP19-255_PUT_3"   "AA83_ASAP69_PD_NP18-287_PUT_3"  
##  [77] "AA_ASAP87_PD_NP21-208_PUT_3"     "AA_ASAP98_ctrl_NP16-119_PUT_3"  
##  [79] "AA_ASAP96_ctrl_NP18-46_PUT_3"    "AA_ASAP88_PD_NP21-217_PUT_3"    
##  [81] "AA82_ASAP68_PD_NP18-117_PUT_3"   "AA73_ASAP65_PD_NP16-269_PUT_3"  
##  [83] "AA81_ASAP67_PD_NP17-191_PUT_3"   "AA71_ASAP70_PD_NP18-304_PUT_3"  
##  [85] "AA77_ASAP61_PD_NP16-25_PUT_3"    "AA_ASAP94_ctrl_NP17-20_PUT_3"   
##  [87] "AA_ASAP92_ctrl_NP16-284_PUT_3"   "AA_ASAP92_ctrl_NP16-284_PUT_5"  
##  [89] "AA78_ASAP63_PD_NP16-160_PUT_5"   "AA_ASAP149_PD_NP23-21_PUT_5"    
##  [91] "AA76_ASAP74_PD_NP19-255_PUT_5"   "AA_ASAP142_ctrl_NP22-37_PUT_5"  
##  [93] "AA_ASAP93_ctrl_NP16-293_PUT_5"   "AA85_ASAP72_PD_NP19-23_PUT_5"   
##  [95] "AA_ASAP88_PD_NP21-217_PUT_5"     "AA88_ASAP77_ctrl_NP19-36_PUT_5" 
##  [97] "AA_ASAP98_ctrl_NP16-119_PUT_5"   "AA74_ASAP62_PD_NP16-140_PUT_5"  
##  [99] "AA82_ASAP68_PD_NP18-117_PUT_5"   "AA73_ASAP65_PD_NP16-269_PUT_5"  
## [101] "AA_ASAP146_PD_NP21-04_PUT_5"     "AA89_ASAP78_ctrl_NP19-37_PUT_5" 
## [103] "AA_ASAP96_ctrl_NP18-46_PUT_5"    "AA_ASAP117_PD_NP22-55_PUT_5"    
## [105] "AA79_ASAP64_PD_NP16-162_PUT_5"   "AA_ASAP94_ctrl_NP17-20_PUT_5"   
## [107] "AA86_ASAP73_PD_NP19-108_PUT_5"   "AA71_ASAP70_PD_NP18-304_PUT_5"  
## [109] "AA_ASAP139_PD_NP17-232_PUT_5"    "AA_ASAP138_PD_NP16-285_PUT_5"   
## [111] "AA_ASAP140_PD_NP19-91_PUT_5"     "AA_ASAP144_PD_NP19-137_PUT_5"   
## [113] "AA_ASAP87_PD_NP21-208_PUT_5"     "AA84_ASAP71_PD_NP19-16_PUT_5"   
## [115] "AA_ASAP141_ctrl_NP19-218_PUT_5"  "AA_ASAP100_ctrl_NP18-148_PUT_5" 
## [117] "AA87_ASAP76_ctrl_NP18-159_PUT_5" "AA_ASAP97_PD_NP21-57_PUT_5"     
## [119] "AA81_ASAP67_PD_NP17-191_PUT_5"   "AA83_ASAP69_PD_NP18-287_PUT_5"  
## [121] "AA77_ASAP61_PD_NP16-25_PUT_5"    "AA89_ASAP78_ctrl_NP19-37_PUT_4" 
## [123] "AA_ASAP94_ctrl_NP17-20_PUT_4"    "AA_ASAP96_ctrl_NP18-46_PUT_4"   
## [125] "AA_ASAP138_PD_NP16-285_PUT_4"    "AA_ASAP141_ctrl_NP19-218_PUT_4" 
## [127] "AA_ASAP140_PD_NP19-91_PUT_4"     "AA79_ASAP64_PD_NP16-162_PUT_4"  
## [129] "AA76_ASAP74_PD_NP19-255_PUT_4"   "AA77_ASAP61_PD_NP16-25_PUT_4"   
## [131] "AA73_ASAP65_PD_NP16-269_PUT_4"   "AA_ASAP88_PD_NP21-217_PUT_4"    
## [133] "AA85_ASAP72_PD_NP19-23_PUT_4"    "AA_ASAP117_PD_NP22-55_PUT_4"    
## [135] "AA_ASAP98_ctrl_NP16-119_PUT_4"   "AA_ASAP87_PD_NP21-208_PUT_4"    
## [137] "AA84_ASAP71_PD_NP19-16_PUT_4"    "AA_ASAP144_PD_NP19-137_PUT_4"   
## [139] "AA_ASAP100_ctrl_NP18-148_PUT_4"  "AA87_ASAP76_ctrl_NP18-159_PUT_4"
## [141] "AA_ASAP97_PD_NP21-57_PUT_4"      "AA71_ASAP70_PD_NP18-304_PUT_4"  
## [143] "AA83_ASAP69_PD_NP18-287_PUT_4"   "AA81_ASAP67_PD_NP17-191_PUT_4"  
## [145] "AA74_ASAP62_PD_NP16-140_PUT_4"  
## 
## $order_rows
##    [1] "HERV_dup940"    "HERV_dup3357"   "HERV_dup379"    "HERV_dup1758"  
##    [5] "HERV_dup1079"   "HERV_dup1708"   "HERV_dup2880"   "HERV_dup2381"  
##    [9] "HERV_dup3375"   "HERV_dup2838"   "HERV_dup3423"   "HERV_dup731"   
##   [13] "HERV_dup1669"   "HERV_dup1000"   "HERV_dup1701"   "HERV_dup2841"  
##   [17] "HERV_dup288"    "HERV_dup3174"   "HERV_dup2491"   "HERV_dup2662"  
##   [21] "HERV_dup474"    "HERV_dup979"    "HERV_dup209"    "HERV_dup1749"  
##   [25] "HERV_dup926"    "HERV_dup3226"   "HERV_dup2158"   "HERV_dup1670"  
##   [29] "HERV_dup518"    "HERV_dup37"     "HERV_dup1309"   "HERV_dup2266"  
##   [33] "HERV_dup384"    "HERV_dup614"    "HERV_dup3252"   "HERV_dup3379"  
##   [37] "HERV_dup1310"   "HERV_dup2752"   "HERV_dup1362"   "HERV_dup1359"  
##   [41] "HERV_dup2847"   "HERV_dup2093"   "HERV_dup562"    "HERV_dup2365"  
##   [45] "HERV_dup202"    "HERV_dup2784"   "HERV_dup218"    "HERV_dup282"   
##   [49] "HERV_dup916"    "HERV_dup2366"   "HERV_dup2292"   "HERV_dup194"   
##   [53] "HERV_dup441"    "HERV_dup115"    "HERV_dup446"    "HERV_dup272"   
##   [57] "HERV_dup1007"   "HERV_dup3355"   "HERV_dup3118"   "HERV_dup1598"  
##   [61] "HERV_dup1437"   "HERV_dup2607"   "HERV_dup18"     "HERV_dup852"   
##   [65] "HERV_dup2353"   "HERV_dup380"    "HERV_dup398"    "HERV_dup215"   
##   [69] "HERV_dup133"    "HERV_dup1943"   "HERV_dup876"    "HERV_dup1036"  
##   [73] "HERV_dup492"    "HERV_dup2599"   "HERV_dup243"    "HERV_dup1752"  
##   [77] "HERV_dup400"    "HERV_dup3179"   "HERV_dup1195"   "HERV_dup2879"  
##   [81] "HERV_dup3335"   "HERV_dup1948"   "HERV_dup565"    "HERV_dup1440"  
##   [85] "HERV_dup369"    "HERV_dup2743"   "HERV_dup1416"   "HERV_dup3363"  
##   [89] "HERV_dup1272"   "HERV_dup3181"   "HERV_dup2250"   "HERV_dup2785"  
##   [93] "HERV_dup2964"   "HERV_dup3143"   "HERV_dup3171"   "HERV_dup1730"  
##   [97] "HERV_dup2320"   "HERV_dup487"    "HERV_dup1089"   "HERV_dup1653"  
##  [101] "HERV_dup573"    "HERV_dup409"    "HERV_dup1208"   "HERV_dup758"   
##  [105] "HERV_dup2188"   "HERV_dup1875"   "HERV_dup350"    "HERV_dup2422"  
##  [109] "HERV_dup1322"   "HERV_dup377"    "HERV_dup890"    "HERV_dup1351"  
##  [113] "HERV_dup1282"   "HERV_dup3124"   "HERV_dup2963"   "HERV_dup2273"  
##  [117] "HERV_dup1417"   "HERV_dup1953"   "HERV_dup2733"   "HERV_dup1569"  
##  [121] "HERV_dup1334"   "HERV_dup1731"   "HERV_dup2166"   "HERV_dup899"   
##  [125] "HERV_dup2235"   "HERV_dup1285"   "HERV_dup386"    "HERV_dup3231"  
##  [129] "HERV_dup2900"   "HERV_dup2736"   "HERV_dup1050"   "HERV_dup2905"  
##  [133] "HERV_dup851"    "HERV_dup1717"   "HERV_dup3148"   "HERV_dup1339"  
##  [137] "HERV_dup2334"   "HERV_dup3522"   "HERV_dup300"    "HERV_dup904"   
##  [141] "HERV_dup2651"   "HERV_dup1114"   "HERV_dup1048"   "HERV_dup2985"  
##  [145] "HERV_dup1394"   "HERV_dup2319"   "HERV_dup2962"   "HERV_dup2772"  
##  [149] "HERV_dup3105"   "HERV_dup1613"   "HERV_dup1333"   "HERV_dup900"   
##  [153] "HERV_dup1433"   "HERV_dup3580"   "HERV_dup2848"   "HERV_dup2855"  
##  [157] "HERV_dup3287"   "HERV_dup2027"   "HERV_dup1052"   "HERV_dup3358"  
##  [161] "HERV_dup1755"   "HERV_dup1082"   "HERV_dup1081"   "HERV_dup2937"  
##  [165] "HERV_dup2149"   "HERV_dup773"    "HERV_dup1804"   "HERV_dup1090"  
##  [169] "HERV_dup2646"   "HERV_dup1298"   "HERV_dup1242"   "HERV_dup151"   
##  [173] "HERV_dup2179"   "HERV_dup2834"   "HERV_dup1890"   "HERV_dup1236"  
##  [177] "HERV_dup1345"   "HERV_dup38"     "HERV_dup2533"   "HERV_dup2163"  
##  [181] "HERV_dup3406"   "HERV_dup2436"   "HERV_dup276"    "HERV_dup2404"  
##  [185] "HERV_dup1657"   "HERV_dup1556"   "HERV_dup1658"   "HERV_dup1662"  
##  [189] "HERV_dup1611"   "HERV_dup301"    "HERV_dup799"    "HERV_dup2525"  
##  [193] "HERV_dup1321"   "HERV_dup2942"   "HERV_dup2383"   "HERV_dup2941"  
##  [197] "HERV_dup1381"   "HERV_dup2152"   "HERV_dup3505"   "HERV_dup3507"  
##  [201] "HERV_dup882"    "HERV_dup2536"   "HERV_dup3270"   "HERV_dup2480"  
##  [205] "HERV_dup803"    "HERV_dup21"     "HERV_dup86"     "HERV_dup930"   
##  [209] "HERV_dup735"    "HERV_dup1851"   "HERV_dup336"    "HERV_dup23"    
##  [213] "HERV_dup3196"   "HERV_dup1273"   "HERV_dup2482"   "HERV_dup2034"  
##  [217] "HERV_dup631"    "HERV_dup2809"   "HERV_dup2977"   "HERV_dup723"   
##  [221] "HERV_dup2183"   "HERV_dup399"    "HERV_dup348"    "HERV_dup831"   
##  [225] "HERV_dup2555"   "HERV_dup3050"   "HERV_dup344"    "HERV_dup2130"  
##  [229] "HERV_dup356"    "HERV_dup977"    "HERV_dup1555"   "HERV_dup982"   
##  [233] "HERV_dup2972"   "HERV_dup251"    "HERV_dup3227"   "HERV_dup551"   
##  [237] "HERV_dup2562"   "HERV_dup1526"   "HERV_dup110"    "HERV_dup1778"  
##  [241] "HERV_dup3013"   "HERV_dup1248"   "HERV_dup1331"   "HERV_dup3031"  
##  [245] "HERV_dup2663"   "HERV_dup2653"   "HERV_dup2278"   "HERV_dup2897"  
##  [249] "HERV_dup1071"   "HERV_dup3694"   "HERV_dup1605"   "HERV_dup1390"  
##  [253] "HERV_dup517"    "HERV_dup3328"   "HERV_dup2356"   "HERV_dup1108"  
##  [257] "HERV_dup2264"   "HERV_dup2033"   "HERV_dup3416"   "HERV_dup2566"  
##  [261] "HERV_dup3117"   "HERV_dup108"    "HERV_dup870"    "HERV_dup1279"  
##  [265] "HERV_dup58"     "HERV_dup968"    "HERV_dup3239"   "HERV_dup152"   
##  [269] "HERV_dup724"    "HERV_dup776"    "HERV_dup1520"   "HERV_dup613"   
##  [273] "HERV_dup554"    "HERV_dup846"    "HERV_dup331"    "HERV_dup1926"  
##  [277] "HERV_dup1304"   "HERV_dup2632"   "HERV_dup1107"   "HERV_dup2797"  
##  [281] "HERV_dup3187"   "HERV_dup3286"   "HERV_dup599"    "HERV_dup127"   
##  [285] "HERV_dup1099"   "HERV_dup5"      "HERV_dup2801"   "HERV_dup1253"  
##  [289] "HERV_dup2778"   "HERV_dup27"     "HERV_dup1720"   "HERV_dup1269"  
##  [293] "HERV_dup2635"   "HERV_dup2391"   "HERV_dup3100"   "HERV_dup662"   
##  [297] "HERV_dup1356"   "HERV_dup1222"   "HERV_dup2843"   "HERV_dup3366"  
##  [301] "HERV_dup3140"   "HERV_dup1346"   "HERV_dup1156"   "HERV_dup1029"  
##  [305] "HERV_dup129"    "HERV_dup118"    "HERV_dup407"    "HERV_dup34"    
##  [309] "HERV_dup1245"   "HERV_dup1366"   "HERV_dup293"    "HERV_dup1587"  
##  [313] "HERV_dup1891"   "HERV_dup1268"   "HERV_dup1412"   "HERV_dup1579"  
##  [317] "HERV_dup1920"   "HERV_dup3519"   "HERV_dup1047"   "HERV_dup1005"  
##  [321] "HERV_dup1532"   "HERV_dup2967"   "HERV_dup433"    "HERV_dup1184"  
##  [325] "HERV_dup1972"   "HERV_dup1364"   "HERV_dup381"    "HERV_dup3394"  
##  [329] "HERV_dup17"     "HERV_dup3037"   "HERV_dup120"    "HERV_dup1962"  
##  [333] "HERV_dup3430"   "HERV_dup2290"   "HERV_dup2529"   "HERV_dup2804"  
##  [337] "HERV_dup1979"   "HERV_dup1640"   "HERV_dup1656"   "HERV_dup3189"  
##  [341] "HERV_dup2378"   "HERV_dup1757"   "HERV_dup3182"   "HERV_dup240"   
##  [345] "HERV_dup2481"   "HERV_dup2823"   "HERV_dup2936"   "HERV_dup924"   
##  [349] "HERV_dup1384"   "HERV_dup3545"   "HERV_dup1103"   "HERV_dup3137"  
##  [353] "HERV_dup2647"   "HERV_dup1131"   "HERV_dup3044"   "HERV_dup2939"  
##  [357] "HERV_dup1210"   "HERV_dup1093"   "HERV_dup2680"   "HERV_dup2875"  
##  [361] "HERV_dup3607"   "HERV_dup1295"   "HERV_dup1187"   "HERV_dup1218"  
##  [365] "HERV_dup2735"   "HERV_dup250"    "HERV_dup710"    "HERV_dup732"   
##  [369] "HERV_dup578"    "HERV_dup591"    "HERV_dup1327"   "HERV_dup1733"  
##  [373] "HERV_dup1302"   "HERV_dup1046"   "HERV_dup1350"   "HERV_dup2728"  
##  [377] "HERV_dup1415"   "HERV_dup1557"   "HERV_dup746"    "HERV_dup3154"  
##  [381] "HERV_dup586"    "HERV_dup2415"   "HERV_dup577"    "HERV_dup736"   
##  [385] "HERV_dup3588"   "HERV_dup1513"   "HERV_dup728"    "HERV_dup2907"  
##  [389] "HERV_dup2878"   "HERV_dup772"    "HERV_dup2604"   "HERV_dup3673"  
##  [393] "HERV_dup572"    "HERV_dup355"    "HERV_dup1438"   "HERV_dup2840"  
##  [397] "HERV_dup1378"   "HERV_dup39"     "HERV_dup1629"   "HERV_dup201"   
##  [401] "HERV_dup2187"   "HERV_dup729"    "HERV_dup3319"   "HERV_dup2886"  
##  [405] "HERV_dup2464"   "HERV_dup1389"   "HERV_dup2696"   "HERV_dup665"   
##  [409] "HERV_dup3008"   "HERV_dup3108"   "HERV_dup1668"   "HERV_dup2945"  
##  [413] "HERV_dup2303"   "HERV_dup443"    "HERV_dup2242"   "HERV_dup3284"  
##  [417] "HERV_dup935"    "HERV_dup57"     "HERV_dup1902"   "HERV_dup981"   
##  [421] "HERV_dup1228"   "HERV_dup2620"   "HERV_dup84"     "HERV_dup508"   
##  [425] "HERV_dup739"    "HERV_dup469"    "HERV_dup682"    "HERV_dup966"   
##  [429] "HERV_dup1514"   "HERV_dup177"    "HERV_dup2603"   "HERV_dup1278"  
##  [433] "HERV_dup183"    "HERV_dup692"    "HERV_dup29"     "HERV_dup2548"  
##  [437] "HERV_dup2857"   "HERV_dup634"    "HERV_dup2747"   "HERV_dup388"   
##  [441] "HERV_dup2706"   "HERV_dup1933"   "HERV_dup1932"   "HERV_dup1212"  
##  [445] "HERV_dup1112"   "HERV_dup1500"   "HERV_dup556"    "HERV_dup2949"  
##  [449] "HERV_dup467"    "HERV_dup184"    "HERV_dup1638"   "HERV_dup1931"  
##  [453] "HERV_dup1073"   "HERV_dup1146"   "HERV_dup1017"   "HERV_dup2141"  
##  [457] "HERV_dup2324"   "HERV_dup2518"   "HERV_dup2100"   "HERV_dup1049"  
##  [461] "HERV_dup530"    "HERV_dup3248"   "HERV_dup595"    "HERV_dup78"    
##  [465] "HERV_dup661"    "HERV_dup2655"   "HERV_dup3688"   "HERV_dup1491"  
##  [469] "HERV_dup3219"   "HERV_dup2337"   "HERV_dup1639"   "HERV_dup1403"  
##  [473] "HERV_dup2272"   "HERV_dup3481"   "HERV_dup1453"   "HERV_dup850"   
##  [477] "HERV_dup570"    "HERV_dup1673"   "HERV_dup180"    "HERV_dup2441"  
##  [481] "HERV_dup1823"   "HERV_dup3073"   "HERV_dup2129"   "HERV_dup314"   
##  [485] "HERV_dup450"    "HERV_dup1213"   "HERV_dup321"    "HERV_dup2217"  
##  [489] "HERV_dup357"    "HERV_dup1239"   "HERV_dup2730"   "HERV_dup1934"  
##  [493] "HERV_dup1374"   "HERV_dup2192"   "HERV_dup3408"   "HERV_dup2602"  
##  [497] "HERV_dup1958"   "HERV_dup1172"   "HERV_dup3131"   "HERV_dup1496"  
##  [501] "HERV_dup3063"   "HERV_dup3015"   "HERV_dup519"    "HERV_dup3016"  
##  [505] "HERV_dup1003"   "HERV_dup568"    "HERV_dup185"    "HERV_dup3606"  
##  [509] "HERV_dup471"    "HERV_dup389"    "HERV_dup2128"   "HERV_dup3217"  
##  [513] "HERV_dup3210"   "HERV_dup2561"   "HERV_dup2159"   "HERV_dup1383"  
##  [517] "HERV_dup894"    "HERV_dup419"    "HERV_dup1617"   "HERV_dup2476"  
##  [521] "HERV_dup2182"   "HERV_dup1447"   "HERV_dup3459"   "HERV_dup626"   
##  [525] "HERV_dup2041"   "HERV_dup640"    "HERV_dup1324"   "HERV_dup934"   
##  [529] "HERV_dup3341"   "HERV_dup2934"   "HERV_dup329"    "HERV_dup1780"  
##  [533] "HERV_dup3107"   "HERV_dup1914"   "HERV_dup1655"   "HERV_dup1707"  
##  [537] "HERV_dup1319"   "HERV_dup2379"   "HERV_dup277"    "HERV_dup2282"  
##  [541] "HERV_dup1868"   "HERV_dup1470"   "HERV_dup873"    "HERV_dup975"   
##  [545] "HERV_dup2530"   "HERV_dup2500"   "HERV_dup112"    "HERV_dup1307"  
##  [549] "HERV_dup632"    "HERV_dup1303"   "HERV_dup1935"   "HERV_dup1614"  
##  [553] "HERV_dup2002"   "HERV_dup1201"   "HERV_dup1661"   "HERV_dup488"   
##  [557] "HERV_dup1923"   "HERV_dup597"    "HERV_dup909"    "HERV_dup3351"  
##  [561] "HERV_dup2891"   "HERV_dup203"    "HERV_dup1413"   "HERV_dup1541"  
##  [565] "HERV_dup1080"   "HERV_dup1316"   "HERV_dup1401"   "HERV_dup1719"  
##  [569] "HERV_dup2112"   "HERV_dup933"    "HERV_dup1240"   "HERV_dup434"   
##  [573] "HERV_dup1750"   "HERV_dup1449"   "HERV_dup969"    "HERV_dup65"    
##  [577] "HERV_dup2739"   "HERV_dup3020"   "HERV_dup2524"   "HERV_dup54"    
##  [581] "HERV_dup671"    "HERV_dup670"    "HERV_dup777"    "HERV_dup2298"  
##  [585] "HERV_dup703"    "HERV_dup214"    "HERV_dup249"    "HERV_dup2012"  
##  [589] "HERV_dup2877"   "HERV_dup2966"   "HERV_dup2019"   "HERV_dup2856"  
##  [593] "HERV_dup2598"   "HERV_dup2299"   "HERV_dup1888"   "HERV_dup1255"  
##  [597] "HERV_dup1232"   "HERV_dup1756"   "HERV_dup1973"   "HERV_dup1283"  
##  [601] "HERV_dup3388"   "HERV_dup3417"   "HERV_dup3390"   "HERV_dup1102"  
##  [605] "HERV_dup2961"   "HERV_dup1297"   "HERV_dup1357"   "HERV_dup1002"  
##  [609] "HERV_dup1484"   "HERV_dup2914"   "HERV_dup954"    "HERV_dup1203"  
##  [613] "HERV_dup2085"   "HERV_dup1694"   "HERV_dup1004"   "HERV_dup1308"  
##  [617] "HERV_dup1917"   "HERV_dup482"    "HERV_dup2438"   "HERV_dup872"   
##  [621] "HERV_dup1317"   "HERV_dup2803"   "HERV_dup1671"   "HERV_dup3365"  
##  [625] "HERV_dup3198"   "HERV_dup2106"   "HERV_dup1281"   "HERV_dup3410"  
##  [629] "HERV_dup1209"   "HERV_dup949"    "HERV_dup3266"   "HERV_dup2695"  
##  [633] "HERV_dup1702"   "HERV_dup3418"   "HERV_dup880"    "HERV_dup1940"  
##  [637] "HERV_dup2261"   "HERV_dup2623"   "HERV_dup612"    "HERV_dup290"   
##  [641] "HERV_dup470"    "HERV_dup468"    "HERV_dup939"    "HERV_dup1982"  
##  [645] "HERV_dup3251"   "HERV_dup2769"   "HERV_dup2588"   "HERV_dup93"    
##  [649] "HERV_dup2589"   "HERV_dup1663"   "HERV_dup1001"   "HERV_dup1846"  
##  [653] "HERV_dup1847"   "HERV_dup980"    "HERV_dup2550"   "HERV_dup1371"  
##  [657] "HERV_dup26"     "HERV_dup94"     "HERV_dup3220"   "HERV_dup1235"  
##  [661] "HERV_dup1243"   "HERV_dup3033"   "HERV_dup2902"   "HERV_dup990"   
##  [665] "HERV_dup956"    "HERV_dup417"    "HERV_dup913"    "HERV_dup2812"  
##  [669] "HERV_dup2631"   "HERV_dup36"     "HERV_dup1512"   "HERV_dup2915"  
##  [673] "HERV_dup3529"   "HERV_dup3343"   "HERV_dup3342"   "HERV_dup1456"  
##  [677] "HERV_dup265"    "HERV_dup1"      "HERV_dup2789"   "HERV_dup1382"  
##  [681] "HERV_dup2643"   "HERV_dup2134"   "HERV_dup61"     "HERV_dup1358"  
##  [685] "HERV_dup302"    "HERV_dup1889"   "HERV_dup600"    "HERV_dup717"   
##  [689] "HERV_dup927"    "HERV_dup2412"   "HERV_dup2376"   "HERV_dup2896"  
##  [693] "HERV_dup2176"   "HERV_dup1596"   "HERV_dup2111"   "HERV_dup1703"  
##  [697] "HERV_dup292"    "HERV_dup1802"   "HERV_dup1315"   "L1PA2_dup39"   
##  [701] "L1PA3_dup9473"  "L1PA2_dup3622"  "L1PA3_dup3502"  "L1HS_dup155"   
##  [705] "L1PA3_dup5418"  "L1HS_dup831"    "L1PA2_dup1621"  "L1PA3_dup2683" 
##  [709] "L1PA2_dup2496"  "L1PA3_dup4884"  "L1PA3_dup4596"  "L1PA2_dup4651" 
##  [713] "L1PA3_dup2662"  "L1PA2_dup595"   "L1PA3_dup6966"  "L1PA3_dup6584" 
##  [717] "L1PA3_dup7792"  "L1PA2_dup1746"  "L1PA3_dup4668"  "L1PA2_dup3405" 
##  [721] "L1PA2_dup678"   "L1PA2_dup994"   "L1PA2_dup2430"  "L1PA3_dup7316" 
##  [725] "L1PA2_dup684"   "L1PA3_dup5594"  "L1PA3_dup1114"  "L1PA3_dup6692" 
##  [729] "L1HS_dup244"    "L1PA2_dup4378"  "L1PA2_dup2261"  "L1PA3_dup10525"
##  [733] "L1HS_dup649"    "L1HS_dup1576"   "L1PA3_dup7947"  "L1PA3_dup3404" 
##  [737] "L1PA3_dup1463"  "L1HS_dup1473"   "L1PA3_dup5825"  "L1PA2_dup382"  
##  [741] "L1PA2_dup472"   "L1PA2_dup2436"  "L1PA2_dup3118"  "L1HS_dup444"   
##  [745] "L1PA2_dup4612"  "L1PA3_dup1943"  "L1HS_dup1437"   "L1PA3_dup9866" 
##  [749] "L1HS_dup370"    "L1PA3_dup840"   "L1HS_dup1501"   "L1PA2_dup1177" 
##  [753] "L1PA3_dup5927"  "L1HS_dup1616"   "L1PA2_dup2004"  "L1PA2_dup3439" 
##  [757] "L1PA2_dup4528"  "L1PA2_dup2127"  "L1PA2_dup4430"  "L1PA2_dup109"  
##  [761] "L1PA2_dup1476"  "L1HS_dup466"    "L1PA3_dup5886"  "L1PA3_dup1046" 
##  [765] "L1PA3_dup1727"  "L1HS_dup376"    "L1HS_dup204"    "L1PA2_dup2444" 
##  [769] "L1PA2_dup4389"  "L1PA2_dup4639"  "L1PA2_dup3629"  "L1PA2_dup726"  
##  [773] "L1HS_dup787"    "L1PA2_dup3426"  "L1PA2_dup732"   "L1HS_dup225"   
##  [777] "L1HS_dup1014"   "L1PA3_dup638"   "L1PA2_dup3160"  "L1HS_dup429"   
##  [781] "L1PA2_dup2504"  "L1HS_dup802"    "L1PA2_dup1049"  "L1HS_dup1284"  
##  [785] "L1PA3_dup247"   "L1PA3_dup9722"  "L1PA3_dup3484"  "L1HS_dup1342"  
##  [789] "L1PA3_dup10072" "L1PA3_dup9702"  "L1PA2_dup3776"  "L1PA2_dup1463" 
##  [793] "L1PA3_dup3959"  "L1PA2_dup2537"  "L1PA3_dup7288"  "L1HS_dup90"    
##  [797] "L1PA3_dup6387"  "L1PA2_dup2168"  "L1PA3_dup7893"  "L1PA2_dup759"  
##  [801] "L1PA2_dup3766"  "L1PA3_dup3586"  "L1PA2_dup1426"  "L1PA2_dup4522" 
##  [805] "L1HS_dup1339"   "L1PA2_dup589"   "L1PA2_dup798"   "L1PA2_dup2180" 
##  [809] "L1PA2_dup2876"  "L1PA3_dup6523"  "L1HS_dup600"    "L1PA3_dup6871" 
##  [813] "L1PA2_dup1490"  "L1PA2_dup1992"  "L1PA2_dup4791"  "L1PA3_dup8117" 
##  [817] "L1HS_dup1514"   "L1PA2_dup4432"  "L1PA2_dup4652"  "L1PA2_dup2565" 
##  [821] "L1PA2_dup4196"  "L1PA2_dup4478"  "L1HS_dup87"     "L1PA3_dup5866" 
##  [825] "L1PA2_dup4611"  "L1PA3_dup1647"  "L1PA2_dup935"   "L1PA3_dup9202" 
##  [829] "L1PA3_dup8891"  "L1PA3_dup4687"  "L1PA3_dup5540"  "L1PA2_dup1112" 
##  [833] "L1PA3_dup3291"  "L1HS_dup111"    "L1HS_dup163"    "L1HS_dup1005"  
##  [837] "L1HS_dup1243"   "L1PA2_dup4421"  "L1PA2_dup4454"  "L1PA3_dup2620" 
##  [841] "L1HS_dup1077"   "L1PA2_dup4335"  "L1PA3_dup1337"  "L1HS_dup622"   
##  [845] "L1HS_dup1295"   "L1PA2_dup219"   "L1PA2_dup3445"  "L1PA3_dup8506" 
##  [849] "L1HS_dup1393"   "L1PA2_dup4936"  "L1PA2_dup2577"  "L1PA3_dup3684" 
##  [853] "L1PA3_dup10043" "L1HS_dup579"    "L1PA2_dup2295"  "L1PA3_dup1989" 
##  [857] "L1PA2_dup4237"  "L1PA3_dup5057"  "L1HS_dup811"    "L1HS_dup1478"  
##  [861] "L1PA2_dup365"   "L1PA2_dup4441"  "L1PA2_dup358"   "L1PA3_dup4349" 
##  [865] "L1PA2_dup4686"  "L1PA2_dup307"   "L1PA3_dup683"   "L1PA3_dup1328" 
##  [869] "L1PA2_dup2047"  "L1PA2_dup4548"  "L1PA2_dup4262"  "L1PA3_dup5363" 
##  [873] "L1HS_dup143"    "L1PA2_dup4713"  "L1PA3_dup4393"  "L1PA3_dup3153" 
##  [877] "L1PA3_dup1528"  "L1PA2_dup1653"  "L1PA2_dup383"   "L1PA2_dup1331" 
##  [881] "L1PA3_dup345"   "L1PA2_dup1050"  "L1PA2_dup2089"  "L1PA2_dup1078" 
##  [885] "L1PA2_dup4201"  "L1HS_dup1020"   "L1PA2_dup1978"  "L1PA3_dup10176"
##  [889] "L1PA2_dup514"   "L1PA3_dup8313"  "L1PA2_dup629"   "L1PA2_dup2506" 
##  [893] "L1PA2_dup4762"  "L1PA3_dup10096" "L1PA2_dup3503"  "L1PA3_dup5047" 
##  [897] "L1HS_dup35"     "L1HS_dup62"     "L1PA2_dup360"   "L1PA2_dup4776" 
##  [901] "L1PA3_dup1279"  "L1PA3_dup5106"  "L1PA3_dup2755"  "L1PA2_dup1248" 
##  [905] "L1HS_dup743"    "L1PA2_dup3930"  "L1PA2_dup4226"  "L1PA3_dup5207" 
##  [909] "L1HS_dup679"    "L1PA2_dup4688"  "L1PA3_dup2389"  "L1HS_dup1357"  
##  [913] "L1HS_dup803"    "L1PA2_dup423"   "L1PA3_dup3005"  "L1PA2_dup747"  
##  [917] "L1PA2_dup1023"  "L1PA3_dup5928"  "L1PA2_dup2581"  "L1PA2_dup2271" 
##  [921] "L1PA3_dup7432"  "L1PA3_dup5544"  "L1PA2_dup4901"  "L1HS_dup1286"  
##  [925] "L1PA2_dup2729"  "L1HS_dup1104"   "L1PA3_dup1550"  "L1PA3_dup9840" 
##  [929] "L1PA2_dup2282"  "L1PA2_dup4309"  "L1PA2_dup4618"  "L1PA3_dup9255" 
##  [933] "L1PA2_dup326"   "L1PA2_dup1058"  "L1PA2_dup675"   "L1PA3_dup5745" 
##  [937] "L1PA2_dup4074"  "L1PA3_dup8173"  "L1PA3_dup5468"  "L1PA2_dup2254" 
##  [941] "L1PA2_dup3484"  "L1PA2_dup727"   "L1PA2_dup3579"  "L1PA3_dup7840" 
##  [945] "L1PA3_dup1428"  "L1HS_dup1182"   "L1PA3_dup10344" "L1PA3_dup4408" 
##  [949] "L1PA3_dup6008"  "L1PA2_dup3283"  "L1HS_dup879"    "L1PA2_dup4045" 
##  [953] "L1HS_dup907"    "L1PA3_dup1027"  "L1PA3_dup1026"  "L1PA3_dup5358" 
##  [957] "L1PA3_dup5355"  "L1PA3_dup3323"  "L1PA3_dup1770"  "L1PA2_dup805"  
##  [961] "L1PA2_dup949"   "L1PA2_dup2408"  "L1PA3_dup8896"  "L1PA2_dup3773" 
##  [965] "L1PA3_dup3300"  "L1PA3_dup3763"  "L1PA2_dup3292"  "L1PA3_dup8328" 
##  [969] "L1PA3_dup6160"  "L1PA2_dup741"   "L1PA3_dup9373"  "L1HS_dup995"   
##  [973] "L1PA2_dup4053"  "L1PA2_dup3003"  "L1PA3_dup9734"  "L1PA2_dup1560" 
##  [977] "L1PA2_dup4043"  "L1PA3_dup10011" "L1PA3_dup6436"  "L1HS_dup1324"  
##  [981] "L1PA3_dup10531" "L1PA2_dup1968"  "L1PA2_dup98"    "L1HS_dup1019"  
##  [985] "L1PA3_dup400"   "L1PA3_dup2643"  "L1PA3_dup3950"  "L1PA3_dup7605" 
##  [989] "L1PA3_dup9856"  "L1PA3_dup3880"  "L1PA3_dup8310"  "L1PA2_dup4030" 
##  [993] "L1PA2_dup1953"  "L1PA2_dup4440"  "L1PA2_dup2969"  "L1PA2_dup1770" 
##  [997] "L1PA2_dup2155"  "L1PA3_dup1269"  "L1PA2_dup1805"  "L1PA3_dup7550" 
## [1001] "L1PA3_dup4708"  "L1PA3_dup5534"  "L1PA3_dup3968"  "L1PA3_dup2393" 
## [1005] "L1PA3_dup5238"  "L1PA3_dup978"   "L1PA3_dup4259"  "L1PA3_dup1554" 
## [1009] "L1PA2_dup2343"  "L1PA2_dup413"   "L1HS_dup270"    "L1PA3_dup3954" 
## [1013] "L1PA3_dup358"   "L1PA2_dup1398"  "L1PA3_dup1547"  "L1PA2_dup2863" 
## [1017] "L1PA3_dup6317"  "L1PA2_dup1375"  "L1PA3_dup8007"  "L1PA3_dup2357" 
## [1021] "L1PA3_dup165"   "L1PA2_dup71"    "L1PA2_dup142"   "L1PA2_dup1933" 
## [1025] "L1PA3_dup4688"  "L1PA3_dup1264"  "L1PA2_dup3607"  "L1PA2_dup3881" 
## [1029] "L1PA2_dup1778"  "L1PA3_dup4709"  "L1PA3_dup1800"  "L1PA2_dup663"  
## [1033] "L1HS_dup1536"   "L1HS_dup632"    "L1PA2_dup559"   "L1PA3_dup4902" 
## [1037] "L1PA2_dup2289"  "L1PA2_dup526"   "L1PA2_dup1418"  "L1PA2_dup378"  
## [1041] "L1PA3_dup398"   "L1PA3_dup7237"  "L1PA3_dup10285" "L1PA3_dup2557" 
## [1045] "L1PA3_dup9095"  "L1PA3_dup4994"  "L1PA2_dup791"   "L1PA3_dup10119"
## [1049] "L1PA3_dup8525"  "L1PA3_dup2517"  "L1PA3_dup1311"  "L1PA3_dup6434" 
## [1053] "L1PA2_dup922"   "L1PA2_dup1230"  "L1PA3_dup2593"  "L1PA3_dup2919" 
## [1057] "L1PA2_dup3664"  "L1PA3_dup8663"  "L1PA3_dup6573"  "L1PA3_dup7470" 
## [1061] "L1PA2_dup234"   "L1PA3_dup2744"  "L1PA2_dup37"    "L1PA2_dup3136" 
## [1065] "L1HS_dup800"    "L1PA2_dup130"   "L1PA3_dup3307"  "L1PA2_dup3805" 
## [1069] "L1PA3_dup3168"  "L1PA3_dup7862"  "L1PA2_dup4620"  "L1HS_dup1462"  
## [1073] "L1PA2_dup4403"  "L1PA2_dup3771"  "L1PA3_dup10297" "L1PA2_dup3589" 
## [1077] "L1HS_dup1330"   "L1PA2_dup1298"  "L1PA2_dup2909"  "L1PA2_dup3736" 
## [1081] "L1PA3_dup4891"  "L1PA3_dup4401"  "L1PA3_dup5680"  "L1PA3_dup7821" 
## [1085] "L1PA2_dup1752"  "L1PA3_dup10740" "L1PA3_dup1710"  "L1PA3_dup4391" 
## [1089] "L1PA3_dup5121"  "L1PA3_dup5514"  "L1PA3_dup3757"  "L1PA3_dup3758" 
## [1093] "L1PA2_dup1272"  "L1PA3_dup1010"  "L1PA3_dup4492"  "L1PA2_dup2245" 
## [1097] "L1PA2_dup927"   "L1PA3_dup373"   "L1PA3_dup1756"  "L1PA3_dup529"  
## [1101] "L1HS_dup455"    "L1PA3_dup2760"  "L1PA2_dup410"   "L1HS_dup514"   
## [1105] "L1PA2_dup2860"  "L1PA2_dup2680"  "L1PA2_dup1462"  "L1PA3_dup2551" 
## [1109] "L1PA3_dup9021"  "L1PA2_dup2091"  "L1PA3_dup6036"  "L1PA2_dup4905" 
## [1113] "L1PA3_dup5337"  "L1PA3_dup9998"  "L1PA3_dup6347"  "L1PA2_dup3437" 
## [1117] "L1PA2_dup3531"  "L1PA3_dup6550"  "L1PA2_dup530"   "L1PA3_dup7864" 
## [1121] "L1PA2_dup3615"  "L1PA3_dup8872"  "L1PA3_dup2721"  "L1PA2_dup4838" 
## [1125] "L1PA2_dup513"   "L1PA2_dup3042"  "L1PA2_dup737"   "L1HS_dup596"   
## [1129] "L1PA3_dup6730"  "L1PA2_dup2385"  "L1PA3_dup4603"  "L1PA3_dup8520" 
## [1133] "L1PA3_dup6929"  "L1PA3_dup9946"  "L1HS_dup124"    "L1PA3_dup6884" 
## [1137] "L1PA2_dup3425"  "L1PA3_dup3729"  "L1PA3_dup3863"  "L1PA3_dup3102" 
## [1141] "L1HS_dup449"    "L1PA3_dup8420"  "L1PA3_dup872"   "L1PA3_dup2039" 
## [1145] "L1PA2_dup4367"  "L1PA2_dup635"   "L1PA2_dup4775"  "L1PA3_dup1952" 
## [1149] "L1PA3_dup761"   "L1PA3_dup6147"  "L1PA3_dup3941"  "L1PA3_dup4804" 
## [1153] "L1PA2_dup2791"  "L1PA3_dup907"   "L1PA3_dup4885"  "L1PA2_dup200"  
## [1157] "L1PA2_dup1379"  "L1HS_dup191"    "L1PA3_dup7951"  "L1PA3_dup6385" 
## [1161] "L1PA3_dup2272"  "L1PA3_dup7472"  "L1PA3_dup7963"  "L1PA2_dup221"  
## [1165] "L1HS_dup788"    "L1PA3_dup6002"  "L1PA2_dup2164"  "L1PA2_dup2988" 
## [1169] "L1HS_dup379"    "L1PA2_dup16"    "L1HS_dup405"    "L1PA2_dup3742" 
## [1173] "L1PA3_dup3507"  "L1PA3_dup9280"  "L1HS_dup138"    "L1HS_dup337"   
## [1177] "L1PA3_dup4122"  "L1PA3_dup2954"  "L1PA2_dup1760"  "L1PA2_dup4714" 
## [1181] "L1PA3_dup1723"  "L1PA3_dup124"   "L1PA3_dup128"   "L1PA3_dup8522" 
## [1185] "L1PA3_dup3509"  "L1PA3_dup1937"  "L1PA3_dup6112"  "L1PA2_dup4596" 
## [1189] "L1PA3_dup4487"  "L1HS_dup948"    "L1PA3_dup3306"  "L1PA3_dup8571" 
## [1193] "L1PA2_dup1749"  "L1PA3_dup9430"  "L1HS_dup916"    "L1PA3_dup561"  
## [1197] "L1PA3_dup1988"  "L1PA3_dup7637"  "L1PA3_dup2204"  "L1PA3_dup5510" 
## [1201] "L1PA3_dup527"   "L1PA2_dup662"   "L1PA2_dup585"   "L1PA2_dup2720" 
## [1205] "L1PA3_dup748"   "L1PA3_dup2413"  "L1HS_dup240"    "L1PA2_dup196"  
## [1209] "L1PA3_dup1"     "L1PA3_dup1651"  "L1PA3_dup4118"  "L1PA3_dup8903" 
## [1213] "L1PA3_dup10686" "L1PA3_dup4888"  "L1PA3_dup4277"  "L1PA2_dup848"  
## [1217] "L1PA3_dup6457"  "L1PA3_dup9256"

asap_heatmap_snRNA(region = c("AMY"), 
                   tes = data_TE_annotation$TE_id, 
                   return_df = F, group_rows = c("type"), gaps_row = length(heatmap_amy_HERV_order),
                   breaks = seq(0,15,length.out = 52), index_row_reorder = c(heatmap_amy_HERV_order,heatmap_amy_L1_order),
                   order_cols_groups = order_cols_celltype,
                   data = TE_data, group_cols = c("celltype"),
                   title = "AMY HERVs + L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
                   exclude_clusters = c(6, 7))

## $heatmap
## 
## $order_cols
##   [1] "DA805_ASAP56_ctrl_NP19-37_AMY_0"  "AA_ASAP115_PD_NP21-208_AMY_0"    
##   [3] "DA474_ASAP24_PD_NP16-25_AMY_0"    "AA_ASAP110_ctrl_NP16-119_AMY_0"  
##   [5] "DA811_ASAP18_PD_NP16-140_AMY_0"   "DA778_ASAP31_PD_NP18-117_AMY_0"  
##   [7] "DA791_ASAP50_ctrl_NP18-159_AMY_0" "DA783_ASAP45_PD_NP19-255_AMY_0"  
##   [9] "DA793_ASAP53_ctrl_NP19-36_AMY_0"  "DA780_ASAP37_PD_NP19-16_AMY_0"   
##  [11] "DA802_ASAP40_PD_NP19-23_AMY_0"    "AA_ASAP114_PD_NP21-57_AMY_0"     
##  [13] "AA_ASAP123_ctrl_NP19-218_AMY_1"   "AA_ASAP124_ctrl_NP22-37_AMY_1"   
##  [15] "AA_ASAP119_PD_NP22-55_AMY_1"      "AA_ASAP114_PD_NP21-57_AMY_1"     
##  [17] "AA_ASAP113_ctrl_NP18-148_AMY_1"   "AA_ASAP121_PD_NP17-232_AMY_1"    
##  [19] "AA_ASAP109_PD_NP21-217_AMY_1"     "AA_ASAP128_PD_NP21-04_AMY_1"     
##  [21] "AA_ASAP131_PD_NP23-21_AMY_1"      "AA_ASAP126_PD_NP19-137_AMY_1"    
##  [23] "DA811_ASAP18_PD_NP16-140_AMY_1"   "DA802_ASAP40_PD_NP19-23_AMY_1"   
##  [25] "DA780_ASAP37_PD_NP19-16_AMY_1"    "DA801_ASAP53_ctrl_NP19-36_AMY_1" 
##  [27] "DA805_ASAP56_ctrl_NP19-37_AMY_1"  "DA474_ASAP24_PD_NP16-25_AMY_1"   
##  [29] "AA_ASAP115_PD_NP21-208_AMY_1"     "AA_ASAP110_ctrl_NP16-119_AMY_1"  
##  [31] "DA512_ASAP60_ctrl_NP19-45_AMY_1"  "DA778_ASAP31_PD_NP18-117_AMY_1"  
##  [33] "DA793_ASAP53_ctrl_NP19-36_AMY_1"  "DA791_ASAP50_ctrl_NP18-159_AMY_1"
##  [35] "DA783_ASAP45_PD_NP19-255_AMY_1"   "ASAP122_PD_NP19-91_AMY_2"        
##  [37] "AA_ASAP109_PD_NP21-217_AMY_2"     "AA_ASAP119_PD_NP22-55_AMY_2"     
##  [39] "AA_ASAP126_PD_NP19-137_AMY_2"     "AA_ASAP131_PD_NP23-21_AMY_2"     
##  [41] "AA_ASAP128_PD_NP21-04_AMY_2"      "DA807_ASAP29_PD_NP17-191_AMY_2"  
##  [43] "DA783_ASAP45_PD_NP19-255_AMY_2"   "AA_ASAP115_PD_NP21-208_AMY_2"    
##  [45] "DA512_ASAP60_ctrl_NP19-45_AMY_2"  "DA474_ASAP24_PD_NP16-25_AMY_2"   
##  [47] "AA_ASAP112_ctrl_NP16-293_AMY_2"   "DA814_ASAP35_PD_NP18-304_AMY_2"  
##  [49] "AA_ASAP120_PD_NP16-285_AMY_2"     "DA811_ASAP18_PD_NP16-140_AMY_2"  
##  [51] "AA_ASAP121_PD_NP17-232_AMY_2"     "AA_ASAP124_ctrl_NP22-37_AMY_2"   
##  [53] "DA791_ASAP50_ctrl_NP18-159_AMY_2" "DA780_ASAP37_PD_NP19-16_AMY_2"   
##  [55] "DA802_ASAP40_PD_NP19-23_AMY_2"    "AA_ASAP123_ctrl_NP19-218_AMY_2"  
##  [57] "DA805_ASAP56_ctrl_NP19-37_AMY_2"  "DA793_ASAP53_ctrl_NP19-36_AMY_2" 
##  [59] "DA801_ASAP53_ctrl_NP19-36_AMY_2"  "DA778_ASAP31_PD_NP18-117_AMY_2"  
##  [61] "AA_ASAP113_ctrl_NP18-148_AMY_2"   "AA_ASAP110_ctrl_NP16-119_AMY_2"  
##  [63] "AA_ASAP114_PD_NP21-57_AMY_2"      "DA783_ASAP45_PD_NP19-255_AMY_3"  
##  [65] "AA_ASAP121_PD_NP17-232_AMY_3"     "AA_ASAP109_PD_NP21-217_AMY_3"    
##  [67] "DA802_ASAP40_PD_NP19-23_AMY_3"    "ASAP122_PD_NP19-91_AMY_3"        
##  [69] "AA_ASAP120_PD_NP16-285_AMY_3"     "AA_ASAP112_ctrl_NP16-293_AMY_3"  
##  [71] "AA_ASAP115_PD_NP21-208_AMY_3"     "AA_ASAP131_PD_NP23-21_AMY_3"     
##  [73] "DA803_ASAP48_ctrl_NP17-256_AMY_3" "AA_ASAP111_ctrl_NP16-284_AMY_3"  
##  [75] "AA_ASAP124_ctrl_NP22-37_AMY_3"    "AA_ASAP119_PD_NP22-55_AMY_3"     
##  [77] "DA807_ASAP29_PD_NP17-191_AMY_3"   "DA811_ASAP18_PD_NP16-140_AMY_3"  
##  [79] "DA805_ASAP56_ctrl_NP19-37_AMY_3"  "AA_ASAP110_ctrl_NP16-119_AMY_3"  
##  [81] "DA474_ASAP24_PD_NP16-25_AMY_3"    "DA801_ASAP53_ctrl_NP19-36_AMY_3" 
##  [83] "DA793_ASAP53_ctrl_NP19-36_AMY_3"  "DA778_ASAP31_PD_NP18-117_AMY_3"  
##  [85] "DA780_ASAP37_PD_NP19-16_AMY_3"    "DA791_ASAP50_ctrl_NP18-159_AMY_3"
##  [87] "AA_ASAP113_ctrl_NP18-148_AMY_3"   "DA512_ASAP60_ctrl_NP19-45_AMY_3" 
##  [89] "AA_ASAP114_PD_NP21-57_AMY_3"      "AA_ASAP123_ctrl_NP19-218_AMY_3"  
##  [91] "AA_ASAP128_PD_NP21-04_AMY_3"      "DA512_ASAP60_ctrl_NP19-45_AMY_5" 
##  [93] "AA_ASAP126_PD_NP19-137_AMY_5"     "AA_ASAP115_PD_NP21-208_AMY_5"    
##  [95] "AA_ASAP110_ctrl_NP16-119_AMY_5"   "DA783_ASAP45_PD_NP19-255_AMY_5"  
##  [97] "DA802_ASAP40_PD_NP19-23_AMY_5"    "DA778_ASAP31_PD_NP18-117_AMY_5"  
##  [99] "AA_ASAP131_PD_NP23-21_AMY_5"      "AA_ASAP121_PD_NP17-232_AMY_5"    
## [101] "DA800_ASAP20_PD_NP16-160_AMY_5"   "AA_ASAP128_PD_NP21-04_AMY_5"     
## [103] "AA_ASAP120_PD_NP16-285_AMY_5"     "DA803_ASAP48_ctrl_NP17-256_AMY_5"
## [105] "ASAP122_PD_NP19-91_AMY_5"         "AA_ASAP109_PD_NP21-217_AMY_5"    
## [107] "DA474_ASAP24_PD_NP16-25_AMY_5"    "DA805_ASAP56_ctrl_NP19-37_AMY_5" 
## [109] "AA_ASAP113_ctrl_NP18-148_AMY_5"   "AA_ASAP114_PD_NP21-57_AMY_5"     
## [111] "DA791_ASAP50_ctrl_NP18-159_AMY_5" "AA_ASAP124_ctrl_NP22-37_AMY_5"   
## [113] "AA_ASAP112_ctrl_NP16-293_AMY_5"   "AA_ASAP119_PD_NP22-55_AMY_5"     
## [115] "DA807_ASAP29_PD_NP17-191_AMY_5"   "DA780_ASAP37_PD_NP19-16_AMY_5"   
## [117] "DA801_ASAP53_ctrl_NP19-36_AMY_5"  "DA793_ASAP53_ctrl_NP19-36_AMY_5" 
## [119] "AA_ASAP123_ctrl_NP19-218_AMY_5"   "DA811_ASAP18_PD_NP16-140_AMY_5"  
## [121] "DA814_ASAP35_PD_NP18-304_AMY_5"   "DA815_ASAP37_PD_NP19-16_AMY_5"   
## [123] "DA779_ASAP33_PD_NP18-287_AMY_5"   "DA802_ASAP40_PD_NP19-23_AMY_4"   
## [125] "DA783_ASAP45_PD_NP19-255_AMY_4"   "AA_ASAP131_PD_NP23-21_AMY_4"     
## [127] "AA_ASAP112_ctrl_NP16-293_AMY_4"   "AA_ASAP115_PD_NP21-208_AMY_4"    
## [129] "DA512_ASAP60_ctrl_NP19-45_AMY_4"  "AA_ASAP126_PD_NP19-137_AMY_4"    
## [131] "DA811_ASAP18_PD_NP16-140_AMY_4"   "DA791_ASAP50_ctrl_NP18-159_AMY_4"
## [133] "DA778_ASAP31_PD_NP18-117_AMY_4"   "DA807_ASAP29_PD_NP17-191_AMY_4"  
## [135] "DA801_ASAP53_ctrl_NP19-36_AMY_4"  "DA805_ASAP56_ctrl_NP19-37_AMY_4" 
## [137] "DA474_ASAP24_PD_NP16-25_AMY_4"    "AA_ASAP119_PD_NP22-55_AMY_4"     
## [139] "AA_ASAP123_ctrl_NP19-218_AMY_4"   "AA_ASAP114_PD_NP21-57_AMY_4"     
## [141] "AA_ASAP113_ctrl_NP18-148_AMY_4"   "DA793_ASAP53_ctrl_NP19-36_AMY_4" 
## [143] "AA_ASAP110_ctrl_NP16-119_AMY_4"  
## 
## $order_rows
##    [1] "HERV_dup3118"   "HERV_dup65"     "HERV_dup670"    "HERV_dup2524"  
##    [5] "HERV_dup671"    "HERV_dup1417"   "HERV_dup417"    "HERV_dup2273"  
##    [9] "HERV_dup3143"   "HERV_dup1613"   "HERV_dup1195"   "HERV_dup350"   
##   [13] "HERV_dup1416"   "HERV_dup2353"   "HERV_dup2422"   "HERV_dup1875"  
##   [17] "HERV_dup2106"   "HERV_dup214"    "HERV_dup1281"   "HERV_dup1209"  
##   [21] "HERV_dup2012"   "HERV_dup2856"   "HERV_dup2966"   "HERV_dup2019"  
##   [25] "HERV_dup249"    "HERV_dup2877"   "HERV_dup36"     "HERV_dup1917"  
##   [29] "HERV_dup3198"   "HERV_dup380"    "HERV_dup3355"   "HERV_dup3505"  
##   [33] "HERV_dup3507"   "HERV_dup1555"   "HERV_dup2378"   "HERV_dup2320"  
##   [37] "HERV_dup2188"   "HERV_dup2743"   "HERV_dup1272"   "HERV_dup1556"  
##   [41] "HERV_dup2555"   "HERV_dup492"    "HERV_dup3335"   "HERV_dup215"   
##   [45] "HERV_dup831"    "HERV_dup3363"   "HERV_dup1948"   "HERV_dup1520"  
##   [49] "HERV_dup3171"   "HERV_dup2646"   "HERV_dup434"    "HERV_dup1658"  
##   [53] "HERV_dup399"    "HERV_dup2809"   "HERV_dup2183"   "HERV_dup723"   
##   [57] "HERV_dup1253"   "HERV_dup3217"   "HERV_dup2977"   "HERV_dup3286"  
##   [61] "HERV_dup1730"   "HERV_dup2696"   "HERV_dup551"    "HERV_dup3227"  
##   [65] "HERV_dup2728"   "HERV_dup23"     "HERV_dup369"    "HERV_dup2879"  
##   [69] "HERV_dup1598"   "HERV_dup2739"   "HERV_dup2163"   "HERV_dup1437"  
##   [73] "HERV_dup2607"   "HERV_dup3351"   "HERV_dup1345"   "HERV_dup1114"  
##   [77] "HERV_dup1351"   "HERV_dup2250"   "HERV_dup1750"   "HERV_dup2848"  
##   [81] "HERV_dup38"     "HERV_dup1868"   "HERV_dup2002"   "HERV_dup2533"  
##   [85] "HERV_dup904"    "HERV_dup1890"   "HERV_dup377"    "HERV_dup2733"  
##   [89] "HERV_dup1243"   "HERV_dup2379"   "HERV_dup1655"   "HERV_dup3459"  
##   [93] "HERV_dup3328"   "HERV_dup873"    "HERV_dup2566"   "HERV_dup3140"  
##   [97] "HERV_dup640"    "HERV_dup2041"   "HERV_dup2897"   "HERV_dup3117"  
##  [101] "HERV_dup3341"   "HERV_dup2934"   "HERV_dup626"    "HERV_dup1447"  
##  [105] "HERV_dup1080"   "HERV_dup2476"   "HERV_dup3231"   "HERV_dup2769"  
##  [109] "HERV_dup1413"   "HERV_dup329"    "HERV_dup2112"   "HERV_dup934"   
##  [113] "HERV_dup3107"   "HERV_dup1703"   "HERV_dup1282"   "HERV_dup1617"  
##  [117] "HERV_dup3251"   "HERV_dup1596"   "HERV_dup1333"   "HERV_dup1719"  
##  [121] "HERV_dup2651"   "HERV_dup2985"   "HERV_dup2962"   "HERV_dup1048"  
##  [125] "HERV_dup300"    "HERV_dup3124"   "HERV_dup2438"   "HERV_dup482"   
##  [129] "HERV_dup94"     "HERV_dup1371"   "HERV_dup1001"   "HERV_dup26"    
##  [133] "HERV_dup980"    "HERV_dup1846"   "HERV_dup1847"   "HERV_dup2550"  
##  [137] "HERV_dup293"    "HERV_dup597"    "HERV_dup799"    "HERV_dup3148"  
##  [141] "HERV_dup909"    "HERV_dup2179"   "HERV_dup1953"   "HERV_dup2500"  
##  [145] "HERV_dup3287"   "HERV_dup990"    "HERV_dup1663"   "HERV_dup2855"  
##  [149] "HERV_dup1512"   "HERV_dup1334"   "HERV_dup899"    "HERV_dup2235"  
##  [153] "HERV_dup1731"   "HERV_dup1569"   "HERV_dup2319"   "HERV_dup2964"  
##  [157] "HERV_dup2282"   "HERV_dup900"    "HERV_dup773"    "HERV_dup3105"  
##  [161] "HERV_dup1235"   "HERV_dup2562"   "HERV_dup2561"   "HERV_dup1236"  
##  [165] "HERV_dup890"    "HERV_dup54"     "HERV_dup2963"   "HERV_dup3220"  
##  [169] "HERV_dup151"    "HERV_dup956"    "HERV_dup1362"   "HERV_dup2404"  
##  [173] "HERV_dup1657"   "HERV_dup1321"   "HERV_dup1319"   "HERV_dup202"   
##  [177] "HERV_dup282"    "HERV_dup218"    "HERV_dup2366"   "HERV_dup2784"  
##  [181] "HERV_dup2292"   "HERV_dup2847"   "HERV_dup2941"   "HERV_dup446"   
##  [185] "HERV_dup2383"   "HERV_dup2942"   "HERV_dup441"    "HERV_dup916"   
##  [189] "HERV_dup572"    "HERV_dup1201"   "HERV_dup1926"   "HERV_dup1532"  
##  [193] "HERV_dup968"    "HERV_dup1605"   "HERV_dup1071"   "HERV_dup1972"  
##  [197] "HERV_dup1156"   "HERV_dup3694"   "HERV_dup1780"   "HERV_dup1304"  
##  [201] "HERV_dup1316"   "HERV_dup2436"   "HERV_dup1324"   "HERV_dup203"   
##  [205] "HERV_dup2278"   "HERV_dup2356"   "HERV_dup3416"   "HERV_dup58"    
##  [209] "HERV_dup108"    "HERV_dup2785"   "HERV_dup3239"   "HERV_dup1541"  
##  [213] "HERV_dup710"    "HERV_dup185"    "HERV_dup3270"   "HERV_dup591"   
##  [217] "HERV_dup433"    "HERV_dup127"    "HERV_dup803"    "HERV_dup3406"  
##  [221] "HERV_dup39"     "HERV_dup2290"   "HERV_dup400"    "HERV_dup1248"  
##  [225] "HERV_dup1089"   "HERV_dup935"    "HERV_dup57"     "HERV_dup398"   
##  [229] "HERV_dup746"    "HERV_dup133"    "HERV_dup1187"   "HERV_dup1210"  
##  [233] "HERV_dup1673"   "HERV_dup1513"   "HERV_dup2187"   "HERV_dup3108"  
##  [237] "HERV_dup381"    "HERV_dup568"    "HERV_dup129"    "HERV_dup728"   
##  [241] "HERV_dup1378"   "HERV_dup1295"   "HERV_dup84"     "HERV_dup1638"  
##  [245] "HERV_dup177"    "HERV_dup1869"   "HERV_dup3481"   "HERV_dup2482"  
##  [249] "HERV_dup1384"   "HERV_dup2557"   "HERV_dup1112"   "HERV_dup1496"  
##  [253] "HERV_dup3073"   "HERV_dup3137"   "HERV_dup1239"   "HERV_dup1639"  
##  [257] "HERV_dup2602"   "HERV_dup1038"   "HERV_dup2464"   "HERV_dup180"   
##  [261] "HERV_dup1958"   "HERV_dup1213"   "HERV_dup2324"   "HERV_dup2192"  
##  [265] "HERV_dup2518"   "HERV_dup2129"   "HERV_dup519"    "HERV_dup1934"  
##  [269] "HERV_dup1374"   "HERV_dup2945"   "HERV_dup966"    "HERV_dup321"   
##  [273] "HERV_dup3131"   "HERV_dup357"    "HERV_dup1724"   "HERV_dup556"   
##  [277] "HERV_dup291"    "HERV_dup2894"   "HERV_dup1668"   "HERV_dup184"   
##  [281] "HERV_dup2875"   "HERV_dup3015"   "HERV_dup1757"   "HERV_dup967"   
##  [285] "HERV_dup1212"   "HERV_dup930"    "HERV_dup1937"   "HERV_dup2655"  
##  [289] "HERV_dup3688"   "HERV_dup3044"   "HERV_dup469"    "HERV_dup419"   
##  [293] "HERV_dup1403"   "HERV_dup1331"   "HERV_dup1500"   "HERV_dup2034"  
##  [297] "HERV_dup3063"   "HERV_dup1587"   "HERV_dup389"    "HERV_dup736"   
##  [301] "HERV_dup2972"   "HERV_dup3154"   "HERV_dup3182"   "HERV_dup34"    
##  [305] "HERV_dup2949"   "HERV_dup505"    "HERV_dup1146"   "HERV_dup924"   
##  [309] "HERV_dup595"    "HERV_dup732"    "HERV_dup729"    "HERV_dup850"   
##  [313] "HERV_dup1415"   "HERV_dup530"    "HERV_dup1933"   "HERV_dup1131"  
##  [317] "HERV_dup1629"   "HERV_dup1278"   "HERV_dup2337"   "HERV_dup2479"  
##  [321] "HERV_dup452"    "HERV_dup86"     "HERV_dup2886"   "HERV_dup2939"  
##  [325] "HERV_dup3008"   "HERV_dup1003"   "HERV_dup1733"   "HERV_dup2878"  
##  [329] "HERV_dup517"    "HERV_dup1005"   "HERV_dup194"    "HERV_dup3219"  
##  [333] "HERV_dup3588"   "HERV_dup3037"   "HERV_dup443"    "HERV_dup1302"  
##  [337] "HERV_dup388"    "HERV_dup2647"   "HERV_dup29"     "HERV_dup2747"  
##  [341] "HERV_dup634"    "HERV_dup554"    "HERV_dup201"    "HERV_dup3016"  
##  [345] "HERV_dup1438"   "HERV_dup2843"   "HERV_dup2303"   "HERV_dup355"   
##  [349] "HERV_dup1920"   "HERV_dup1366"   "HERV_dup894"    "HERV_dup2967"  
##  [353] "HERV_dup115"    "HERV_dup272"    "HERV_dup467"    "HERV_dup1007"  
##  [357] "HERV_dup1108"   "HERV_dup2706"   "HERV_dup682"    "HERV_dup2620"  
##  [361] "HERV_dup450"    "HERV_dup2603"   "HERV_dup1514"   "HERV_dup2272"  
##  [365] "HERV_dup2441"   "HERV_dup3606"   "HERV_dup1073"   "HERV_dup1228"  
##  [369] "HERV_dup183"    "HERV_dup2857"   "HERV_dup1245"   "HERV_dup471"   
##  [373] "HERV_dup2548"   "HERV_dup1389"   "HERV_dup1412"   "HERV_dup3519"  
##  [377] "HERV_dup1327"   "HERV_dup3210"   "HERV_dup1653"   "HERV_dup2907"  
##  [381] "HERV_dup2264"   "HERV_dup2033"   "HERV_dup2804"   "HERV_dup692"   
##  [385] "HERV_dup1279"   "HERV_dup1017"   "HERV_dup2100"   "HERV_dup1640"  
##  [389] "HERV_dup3673"   "HERV_dup17"     "HERV_dup1656"   "HERV_dup1979"  
##  [393] "HERV_dup344"    "HERV_dup870"    "HERV_dup2529"   "HERV_dup1390"  
##  [397] "HERV_dup1222"   "HERV_dup2937"   "HERV_dup2536"   "HERV_dup356"   
##  [401] "HERV_dup1470"   "HERV_dup331"    "HERV_dup662"    "HERV_dup1891"  
##  [405] "HERV_dup1720"   "HERV_dup2891"   "HERV_dup1047"   "HERV_dup3394"  
##  [409] "HERV_dup120"    "HERV_dup301"    "HERV_dup724"    "HERV_dup2152"  
##  [413] "HERV_dup2635"   "HERV_dup3366"   "HERV_dup599"    "HERV_dup1052"  
##  [417] "HERV_dup2599"   "HERV_dup1298"   "HERV_dup1804"   "HERV_dup975"   
##  [421] "HERV_dup1943"   "HERV_dup1611"   "HERV_dup243"    "HERV_dup1356"  
##  [425] "HERV_dup2391"   "HERV_dup776"    "HERV_dup407"    "HERV_dup1268"  
##  [429] "HERV_dup152"    "HERV_dup613"    "HERV_dup2604"   "HERV_dup118"   
##  [433] "HERV_dup3179"   "HERV_dup2149"   "HERV_dup1090"   "HERV_dup846"   
##  [437] "HERV_dup573"    "HERV_dup933"    "HERV_dup1029"   "HERV_dup1242"  
##  [441] "HERV_dup3181"   "HERV_dup2631"   "HERV_dup1433"   "HERV_dup3580"  
##  [445] "HERV_dup1381"   "HERV_dup852"    "HERV_dup18"     "HERV_dup3430"  
##  [449] "HERV_dup2663"   "HERV_dup2653"   "HERV_dup3013"   "HERV_dup1778"  
##  [453] "HERV_dup3031"   "HERV_dup3050"   "HERV_dup1962"   "HERV_dup977"   
##  [457] "HERV_dup882"    "HERV_dup2130"   "HERV_dup565"    "HERV_dup2480"  
##  [461] "HERV_dup348"    "HERV_dup1453"   "HERV_dup336"    "HERV_dup251"   
##  [465] "HERV_dup508"    "HERV_dup631"    "HERV_dup2632"   "HERV_dup1346"  
##  [469] "HERV_dup1107"   "HERV_dup1526"   "HERV_dup5"      "HERV_dup1752"  
##  [473] "HERV_dup250"    "HERV_dup1208"   "HERV_dup3100"   "HERV_dup1184"  
##  [477] "HERV_dup1661"   "HERV_dup487"    "HERV_dup2159"   "HERV_dup1755"  
##  [481] "HERV_dup981"    "HERV_dup577"    "HERV_dup1099"   "HERV_dup2840"  
##  [485] "HERV_dup1491"   "HERV_dup21"     "HERV_dup1273"   "HERV_dup586"   
##  [489] "HERV_dup982"    "HERV_dup735"    "HERV_dup1103"   "HERV_dup2936"  
##  [493] "HERV_dup665"    "HERV_dup1851"   "HERV_dup3284"   "HERV_dup1049"  
##  [497] "HERV_dup1218"   "HERV_dup1093"   "HERV_dup570"    "HERV_dup2823"  
##  [501] "HERV_dup3212"   "HERV_dup1902"   "HERV_dup3215"   "HERV_dup2242"  
##  [505] "HERV_dup1579"   "HERV_dup3187"   "HERV_dup2415"   "HERV_dup2730"  
##  [509] "HERV_dup1036"   "HERV_dup3196"   "HERV_dup1932"   "HERV_dup2978"  
##  [513] "HERV_dup2979"   "HERV_dup3189"   "HERV_dup1823"   "HERV_dup1459"  
##  [517] "HERV_dup1350"   "HERV_dup1064"   "HERV_dup1046"   "HERV_dup876"   
##  [521] "HERV_dup2735"   "HERV_dup1440"   "HERV_dup578"    "HERV_dup1383"  
##  [525] "HERV_dup1303"   "HERV_dup1935"   "HERV_dup2128"   "HERV_dup2680"  
##  [529] "HERV_dup3319"   "HERV_dup1557"   "HERV_dup2778"   "HERV_dup110"   
##  [533] "HERV_dup2530"   "HERV_dup277"    "HERV_dup1401"   "HERV_dup1364"  
##  [537] "HERV_dup2797"   "HERV_dup1707"   "HERV_dup1914"   "HERV_dup1082"  
##  [541] "HERV_dup1081"   "HERV_dup409"    "HERV_dup2736"   "HERV_dup3358"  
##  [545] "HERV_dup2905"   "HERV_dup1269"   "HERV_dup488"    "HERV_dup27"    
##  [549] "HERV_dup2801"   "HERV_dup703"    "HERV_dup851"    "HERV_dup2334"  
##  [553] "HERV_dup2166"   "HERV_dup1050"   "HERV_dup2900"   "HERV_dup386"   
##  [557] "HERV_dup1717"   "HERV_dup1285"   "HERV_dup632"    "HERV_dup1339"  
##  [561] "HERV_dup1240"   "HERV_dup112"    "HERV_dup2182"   "HERV_dup2027"  
##  [565] "HERV_dup3522"   "HERV_dup2772"   "HERV_dup276"    "HERV_dup1614"  
##  [569] "HERV_dup1322"   "HERV_dup2525"   "HERV_dup2834"   "HERV_dup758"   
##  [573] "HERV_dup1307"   "HERV_dup1662"   "HERV_dup1923"   "HERV_dup1359"  
##  [577] "HERV_dup2093"   "HERV_dup2365"   "HERV_dup562"    "HERV_dup777"   
##  [581] "HERV_dup1394"   "HERV_dup2298"   "HERV_dup2376"   "HERV_dup2896"  
##  [585] "HERV_dup93"     "HERV_dup2588"   "HERV_dup2589"   "HERV_dup2176"  
##  [589] "HERV_dup1802"   "HERV_dup2111"   "HERV_dup880"    "HERV_dup3365"  
##  [593] "HERV_dup1940"   "HERV_dup2643"   "HERV_dup292"    "HERV_dup1456"  
##  [597] "HERV_dup2598"   "HERV_dup1315"   "HERV_dup290"    "HERV_dup1317"  
##  [601] "HERV_dup2623"   "HERV_dup2803"   "HERV_dup1671"   "HERV_dup1232"  
##  [605] "HERV_dup1888"   "HERV_dup2261"   "HERV_dup1382"   "HERV_dup872"   
##  [609] "HERV_dup1973"   "HERV_dup1102"   "HERV_dup1357"   "HERV_dup3390"  
##  [613] "HERV_dup954"    "HERV_dup1297"   "HERV_dup1484"   "HERV_dup2914"  
##  [617] "HERV_dup3266"   "HERV_dup2085"   "HERV_dup3410"   "HERV_dup1694"  
##  [621] "HERV_dup1004"   "HERV_dup949"    "HERV_dup1203"   "HERV_dup939"   
##  [625] "HERV_dup470"    "HERV_dup468"    "HERV_dup2915"   "HERV_dup612"   
##  [629] "HERV_dup474"    "HERV_dup2902"   "HERV_dup1982"   "HERV_dup2299"  
##  [633] "HERV_dup2695"   "HERV_dup1702"   "HERV_dup3418"   "HERV_dup3529"  
##  [637] "HERV_dup518"    "HERV_dup3379"   "HERV_dup3226"   "HERV_dup1310"  
##  [641] "HERV_dup2752"   "HERV_dup2158"   "HERV_dup1756"   "HERV_dup302"   
##  [645] "HERV_dup1889"   "HERV_dup1283"   "HERV_dup717"    "HERV_dup600"   
##  [649] "HERV_dup2412"   "HERV_dup2961"   "HERV_dup1002"   "HERV_dup927"   
##  [653] "HERV_dup1670"   "HERV_dup1308"   "HERV_dup3388"   "HERV_dup3417"  
##  [657] "HERV_dup384"    "HERV_dup2266"   "HERV_dup1309"   "HERV_dup37"    
##  [661] "HERV_dup61"     "HERV_dup3174"   "HERV_dup3423"   "HERV_dup2491"  
##  [665] "HERV_dup3343"   "HERV_dup3342"   "HERV_dup2789"   "HERV_dup1"     
##  [669] "HERV_dup265"    "HERV_dup1358"   "HERV_dup2134"   "HERV_dup940"   
##  [673] "HERV_dup3252"   "HERV_dup614"    "HERV_dup2662"   "HERV_dup2841"  
##  [677] "HERV_dup288"    "HERV_dup1000"   "HERV_dup1669"   "HERV_dup1701"  
##  [681] "HERV_dup731"    "HERV_dup3375"   "HERV_dup379"    "HERV_dup3357"  
##  [685] "HERV_dup2838"   "HERV_dup1758"   "HERV_dup1079"   "HERV_dup1708"  
##  [689] "HERV_dup2880"   "HERV_dup2381"   "HERV_dup1255"   "HERV_dup926"   
##  [693] "HERV_dup913"    "HERV_dup1749"   "HERV_dup2812"   "HERV_dup3033"  
##  [697] "HERV_dup979"    "HERV_dup3020"   "HERV_dup1449"   "HERV_dup969"   
##  [701] "HERV_dup209"    "L1PA3_dup3763"  "L1HS_dup62"     "L1PA2_dup1375" 
##  [705] "L1PA3_dup7432"  "L1PA2_dup1621"  "L1PA2_dup4043"  "L1PA3_dup8313" 
##  [709] "L1PA2_dup3622"  "L1PA2_dup2496"  "L1PA2_dup4309"  "L1HS_dup405"   
##  [713] "L1PA2_dup1746"  "L1PA2_dup39"    "L1PA3_dup1723"  "L1PA3_dup4884" 
##  [717] "L1PA2_dup4651"  "L1PA3_dup3509"  "L1PA2_dup2343"  "L1PA3_dup1554" 
##  [721] "L1PA2_dup4226"  "L1PA3_dup2683"  "L1PA3_dup6160"  "L1PA2_dup595"  
##  [725] "L1PA2_dup678"   "L1PA2_dup326"   "L1PA3_dup10176" "L1PA3_dup2954" 
##  [729] "L1PA3_dup4596"  "L1PA2_dup3003"  "L1HS_dup916"    "L1PA2_dup4053" 
##  [733] "L1PA3_dup8328"  "L1PA2_dup741"   "L1PA3_dup9373"  "L1PA3_dup6584" 
##  [737] "L1PA3_dup3502"  "L1PA3_dup10344" "L1PA3_dup7792"  "L1PA2_dup16"   
##  [741] "L1PA2_dup1560"  "L1PA3_dup4668"  "L1PA3_dup5418"  "L1PA2_dup2581" 
##  [745] "L1HS_dup155"    "L1PA3_dup7864"  "L1PA2_dup3615"  "L1PA2_dup2155" 
##  [749] "L1PA2_dup4714"  "L1PA2_dup2969"  "L1PA3_dup8522"  "L1PA2_dup4440" 
##  [753] "L1PA2_dup1749"  "L1PA3_dup1988"  "L1PA2_dup4596"  "L1PA3_dup4487" 
##  [757] "L1PA2_dup4775"  "L1PA3_dup1952"  "L1HS_dup379"    "L1PA2_dup3742" 
##  [761] "L1HS_dup948"    "L1PA3_dup1937"  "L1PA3_dup6112"  "L1PA3_dup3306" 
##  [765] "L1PA3_dup7316"  "L1PA2_dup4905"  "L1PA2_dup1653"  "L1PA3_dup1027" 
##  [769] "L1PA3_dup6929"  "L1PA3_dup9998"  "L1PA3_dup5745"  "L1PA3_dup3307" 
##  [773] "L1PA2_dup3042"  "L1PA3_dup6347"  "L1PA3_dup5468"  "L1PA2_dup3579" 
##  [777] "L1PA2_dup2254"  "L1PA3_dup1550"  "L1PA2_dup727"   "L1PA2_dup3484" 
##  [781] "L1PA2_dup675"   "L1PA2_dup4074"  "L1PA3_dup7840"  "L1PA3_dup8173" 
##  [785] "L1PA3_dup9946"  "L1PA3_dup3323"  "L1PA3_dup3300"  "L1PA3_dup8420" 
##  [789] "L1PA3_dup1428"  "L1PA3_dup1463"  "L1PA3_dup3950"  "L1PA2_dup4936" 
##  [793] "L1PA3_dup4408"  "L1PA3_dup3880"  "L1PA2_dup1331"  "L1PA2_dup949"  
##  [797] "L1PA2_dup1078"  "L1HS_dup1104"   "L1HS_dup907"    "L1HS_dup1324"  
##  [801] "L1PA2_dup684"   "L1PA2_dup2577"  "L1PA3_dup1528"  "L1PA3_dup8896" 
##  [805] "L1PA2_dup4045"  "L1PA3_dup5358"  "L1PA3_dup5355"  "L1PA3_dup6884" 
##  [809] "L1PA3_dup1770"  "L1HS_dup124"    "L1PA2_dup805"   "L1PA2_dup3773" 
##  [813] "L1PA3_dup400"   "L1PA3_dup10072" "L1PA3_dup1026"  "L1PA3_dup3484" 
##  [817] "L1PA3_dup4393"  "L1PA3_dup9722"  "L1HS_dup879"    "L1PA3_dup2643" 
##  [821] "L1PA3_dup9856"  "L1PA3_dup6008"  "L1PA3_dup3729"  "L1PA2_dup3425" 
##  [825] "L1PA3_dup3954"  "L1PA3_dup1547"  "L1PA2_dup413"   "L1PA3_dup10525"
##  [829] "L1PA3_dup6317"  "L1PA3_dup9255"  "L1PA3_dup9840"  "L1PA2_dup2863" 
##  [833] "L1PA3_dup10096" "L1PA2_dup1770"  "L1PA2_dup994"   "L1PA2_dup2430" 
##  [837] "L1PA3_dup5047"  "L1HS_dup831"    "L1PA2_dup3503"  "L1PA2_dup219"  
##  [841] "L1PA2_dup4688"  "L1PA2_dup747"   "L1PA3_dup5106"  "L1PA2_dup514"  
##  [845] "L1HS_dup1005"   "L1HS_dup995"    "L1PA2_dup383"   "L1PA2_dup1112" 
##  [849] "L1PA3_dup4259"  "L1PA3_dup5866"  "L1PA3_dup2755"  "L1HS_dup270"   
##  [853] "L1PA3_dup1279"  "L1PA3_dup3005"  "L1PA2_dup4454"  "L1HS_dup225"   
##  [857] "L1HS_dup649"    "L1HS_dup811"    "L1PA3_dup6387"  "L1PA3_dup8506" 
##  [861] "L1PA2_dup4762"  "L1PA3_dup7947"  "L1PA2_dup2089"  "L1PA2_dup2729" 
##  [865] "L1HS_dup579"    "L1HS_dup1295"   "L1HS_dup1020"   "L1PA2_dup3445" 
##  [869] "L1PA3_dup5928"  "L1PA3_dup5927"  "L1PA2_dup4686"  "L1PA3_dup1989" 
##  [873] "L1PA2_dup3776"  "L1PA3_dup6692"  "L1PA2_dup2282"  "L1PA2_dup2295" 
##  [877] "L1PA2_dup629"   "L1HS_dup787"    "L1PA2_dup360"   "L1PA2_dup358"  
##  [881] "L1PA2_dup2168"  "L1PA2_dup2506"  "L1PA3_dup1328"  "L1HS_dup622"   
##  [885] "L1PA2_dup1426"  "L1PA3_dup345"   "L1PA3_dup10043" "L1PA2_dup4522" 
##  [889] "L1PA2_dup4639"  "L1HS_dup370"    "L1PA2_dup4611"  "L1HS_dup1393"  
##  [893] "L1PA2_dup4201"  "L1PA3_dup7893"  "L1HS_dup1243"   "L1PA3_dup5594" 
##  [897] "L1HS_dup90"     "L1PA2_dup2565"  "L1PA2_dup759"   "L1PA2_dup726"  
##  [901] "L1PA3_dup247"   "L1HS_dup244"    "L1HS_dup1514"   "L1PA2_dup1463" 
##  [905] "L1HS_dup1077"   "L1PA3_dup2389"  "L1HS_dup679"    "L1PA3_dup638"  
##  [909] "L1PA2_dup4548"  "L1HS_dup466"    "L1PA2_dup1476"  "L1PA2_dup2047" 
##  [913] "L1HS_dup111"    "L1PA2_dup4378"  "L1PA2_dup2180"  "L1PA3_dup10531"
##  [917] "L1PA3_dup1046"  "L1PA3_dup8117"  "L1PA3_dup3404"  "L1PA3_dup9202" 
##  [921] "L1HS_dup1342"   "L1PA2_dup2004"  "L1PA2_dup1177"  "L1PA3_dup6871" 
##  [925] "L1PA2_dup4612"  "L1PA2_dup4430"  "L1HS_dup163"    "L1PA2_dup1992" 
##  [929] "L1PA3_dup5363"  "L1PA3_dup3153"  "L1HS_dup1339"   "L1PA2_dup3439" 
##  [933] "L1PA2_dup4196"  "L1PA3_dup5886"  "L1PA2_dup935"   "L1PA2_dup4713" 
##  [937] "L1PA2_dup1398"  "L1PA2_dup1490"  "L1PA3_dup3684"  "L1PA2_dup3160" 
##  [941] "L1PA2_dup109"   "L1PA2_dup307"   "L1PA3_dup1647"  "L1PA2_dup732"  
##  [945] "L1PA2_dup2436"  "L1PA3_dup5540"  "L1PA2_dup3426"  "L1PA3_dup840"  
##  [949] "L1PA3_dup9866"  "L1PA3_dup1727"  "L1HS_dup802"    "L1PA3_dup683"  
##  [953] "L1HS_dup429"    "L1PA2_dup4791"  "L1PA2_dup4652"  "L1HS_dup1616"  
##  [957] "L1HS_dup204"    "L1PA3_dup5825"  "L1HS_dup87"     "L1PA2_dup2504" 
##  [961] "L1PA2_dup4528"  "L1PA2_dup4432"  "L1PA3_dup3959"  "L1HS_dup1473"  
##  [965] "L1HS_dup444"    "L1PA3_dup6523"  "L1PA2_dup798"   "L1HS_dup143"   
##  [969] "L1PA3_dup3586"  "L1PA2_dup589"   "L1PA2_dup3766"  "L1PA2_dup3629" 
##  [973] "L1PA2_dup2876"  "L1PA2_dup382"   "L1HS_dup1014"   "L1PA3_dup9702" 
##  [977] "L1HS_dup376"    "L1HS_dup1437"   "L1PA2_dup2127"  "L1PA2_dup4478" 
##  [981] "L1PA2_dup4389"  "L1PA2_dup2444"  "L1PA3_dup1943"  "L1HS_dup1284"  
##  [985] "L1PA2_dup2537"  "L1PA2_dup3118"  "L1HS_dup1491"   "L1PA2_dup472"  
##  [989] "L1HS_dup1501"   "L1PA2_dup1049"  "L1PA2_dup2261"  "L1PA3_dup7288" 
##  [993] "L1PA3_dup4687"  "L1PA3_dup3291"  "L1PA3_dup8891"  "L1HS_dup600"   
##  [997] "L1PA3_dup10011" "L1HS_dup35"     "L1PA2_dup1023"  "L1HS_dup1286"  
## [1001] "L1PA3_dup5207"  "L1PA2_dup1248"  "L1PA2_dup3930"  "L1PA2_dup3292" 
## [1005] "L1PA2_dup4901"  "L1PA2_dup1050"  "L1PA3_dup5544"  "L1PA3_dup4349" 
## [1009] "L1PA2_dup2271"  "L1PA2_dup1978"  "L1HS_dup1576"   "L1PA2_dup365"  
## [1013] "L1PA2_dup423"   "L1PA2_dup4618"  "L1HS_dup743"    "L1HS_dup1019"  
## [1017] "L1PA2_dup4262"  "L1PA2_dup3283"  "L1PA3_dup7605"  "L1PA2_dup4776" 
## [1021] "L1HS_dup1478"   "L1PA2_dup4237"  "L1HS_dup1357"   "L1PA3_dup1337" 
## [1025] "L1PA2_dup4421"  "L1PA3_dup6436"  "L1PA2_dup2408"  "L1PA2_dup1968" 
## [1029] "L1PA3_dup5057"  "L1HS_dup803"    "L1PA3_dup2620"  "L1PA2_dup4441" 
## [1033] "L1PA2_dup4335"  "L1PA2_dup98"    "L1PA3_dup8310"  "L1PA2_dup1953" 
## [1037] "L1PA2_dup1805"  "L1PA3_dup1114"  "L1PA2_dup4030"  "L1PA2_dup1058" 
## [1041] "L1PA3_dup4708"  "L1PA3_dup5534"  "L1PA3_dup1269"  "L1PA3_dup3968" 
## [1045] "L1PA3_dup7550"  "L1PA2_dup1778"  "L1PA2_dup3405"  "L1PA3_dup1264" 
## [1049] "L1PA3_dup9473"  "L1PA3_dup4688"  "L1PA2_dup3607"  "L1PA2_dup3881" 
## [1053] "L1PA3_dup4709"  "L1PA3_dup1800"  "L1PA3_dup9095"  "L1PA2_dup3437" 
## [1057] "L1PA3_dup5238"  "L1PA3_dup8007"  "L1PA3_dup978"   "L1PA3_dup165"  
## [1061] "L1PA2_dup71"    "L1PA3_dup2393"  "L1PA2_dup142"   "L1PA3_dup358"  
## [1065] "L1PA2_dup1933"  "L1PA3_dup2357"  "L1PA2_dup662"   "L1PA2_dup585"  
## [1069] "L1PA3_dup2760"  "L1PA2_dup2680"  "L1HS_dup455"    "L1PA3_dup527"  
## [1073] "L1HS_dup514"    "L1PA2_dup1462"  "L1PA2_dup410"   "L1PA2_dup1379" 
## [1077] "L1PA3_dup561"   "L1PA3_dup872"   "L1PA3_dup2039"  "L1PA3_dup4804" 
## [1081] "L1PA2_dup2988"  "L1PA3_dup3941"  "L1PA3_dup5121"  "L1PA3_dup5514" 
## [1085] "L1PA3_dup3757"  "L1PA3_dup3758"  "L1PA2_dup4367"  "L1PA3_dup128"  
## [1089] "L1PA3_dup124"   "L1HS_dup337"    "L1PA3_dup4122"  "L1PA3_dup907"  
## [1093] "L1PA3_dup9280"  "L1PA2_dup200"   "L1PA3_dup7637"  "L1PA2_dup559"  
## [1097] "L1PA2_dup2860"  "L1PA3_dup4902"  "L1PA2_dup2289"  "L1PA3_dup4885" 
## [1101] "L1PA2_dup2791"  "L1PA2_dup635"   "L1PA3_dup2272"  "L1PA3_dup6385" 
## [1105] "L1PA2_dup4620"  "L1PA3_dup5680"  "L1PA2_dup2909"  "L1HS_dup1462"  
## [1109] "L1PA3_dup10740" "L1PA2_dup3771"  "L1PA2_dup2164"  "L1PA2_dup1298" 
## [1113] "L1PA3_dup4891"  "L1PA2_dup3589"  "L1PA3_dup7862"  "L1PA2_dup1752" 
## [1117] "L1PA3_dup7963"  "L1PA3_dup7472"  "L1PA3_dup1710"  "L1PA3_dup4401" 
## [1121] "L1PA2_dup3805"  "L1HS_dup788"    "L1PA2_dup221"   "L1PA2_dup3736" 
## [1125] "L1PA3_dup7821"  "L1HS_dup1330"   "L1PA3_dup6002"  "L1PA3_dup7951" 
## [1129] "L1HS_dup191"    "L1PA3_dup3507"  "L1PA3_dup3168"  "L1PA3_dup4391" 
## [1133] "L1PA2_dup663"   "L1HS_dup1536"   "L1HS_dup632"    "L1PA2_dup526"  
## [1137] "L1PA2_dup1418"  "L1PA2_dup2720"  "L1PA3_dup7237"  "L1PA3_dup1010" 
## [1141] "L1PA3_dup1311"  "L1PA3_dup4994"  "L1PA2_dup922"   "L1PA2_dup1230" 
## [1145] "L1PA3_dup2593"  "L1PA3_dup8663"  "L1PA3_dup2919"  "L1PA3_dup4277" 
## [1149] "L1PA3_dup2557"  "L1PA2_dup2245"  "L1PA2_dup927"   "L1PA3_dup373"  
## [1153] "L1PA3_dup529"   "L1PA3_dup1756"  "L1PA2_dup1272"  "L1PA2_dup791"  
## [1157] "L1PA3_dup10119" "L1PA3_dup10285" "L1PA3_dup8525"  "L1PA3_dup6966" 
## [1161] "L1PA3_dup6730"  "L1HS_dup596"    "L1PA2_dup737"   "L1PA2_dup4838" 
## [1165] "L1PA2_dup513"   "L1PA3_dup9430"  "L1PA3_dup8571"  "L1PA3_dup2204" 
## [1169] "L1PA3_dup8520"  "L1PA3_dup4603"  "L1PA3_dup3102"  "L1HS_dup449"   
## [1173] "L1PA3_dup2721"  "L1PA2_dup2385"  "L1PA3_dup8872"  "L1PA3_dup3863" 
## [1177] "L1PA2_dup1760"  "L1PA3_dup5510"  "L1PA3_dup2662"  "L1PA3_dup9734" 
## [1181] "L1PA3_dup6147"  "L1HS_dup1182"   "L1HS_dup138"    "L1PA2_dup3531" 
## [1185] "L1PA3_dup7470"  "L1PA3_dup6550"  "L1PA2_dup234"   "L1PA3_dup761"  
## [1189] "L1PA3_dup2517"  "L1PA3_dup5337"  "L1PA3_dup6573"  "L1PA2_dup37"   
## [1193] "L1PA2_dup3136"  "L1HS_dup800"    "L1PA2_dup3664"  "L1PA3_dup6434" 
## [1197] "L1PA2_dup378"   "L1PA3_dup398"   "L1PA3_dup2744"  "L1PA2_dup530"  
## [1201] "L1PA3_dup2413"  "L1PA3_dup748"   "L1PA3_dup4492"  "L1PA2_dup130"  
## [1205] "L1PA3_dup6036"  "L1PA2_dup2091"  "L1PA3_dup9021"  "L1PA3_dup2551" 
## [1209] "L1PA2_dup848"   "L1PA3_dup6457"  "L1PA3_dup4888"  "L1PA3_dup10686"
## [1213] "L1PA3_dup8903"  "L1HS_dup240"    "L1PA2_dup196"   "L1PA3_dup1"    
## [1217] "L1PA3_dup4118"  "L1PA2_dup4403"  "L1PA3_dup1651"  "L1PA3_dup10297"
## [1221] "L1PA3_dup9256"

asap_heatmap_snRNA(region = c("SN"), 
                   tes = data_TE_annotation$TE_id, 
                   return_df = F, group_rows = c("type"), gaps_row = length(heatmap_sn_HERV_order),
                   breaks = seq(0,15,length.out = 52), index_row_reorder = c(heatmap_sn_HERV_order,heatmap_sn_L1_order),
                   order_cols_groups = order_cols_celltype,
                   data = TE_data, group_cols = c("celltype"),
                   title = "SN HERVs + L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
                   exclude_clusters = c(6, 7))

## $heatmap
## 
## $order_cols
##   [1] "AA_ASAP129_ctrl_NP22-37_SN_1"    "AA_ASAP118_PD_NP22-55_SN_1"     
##   [3] "DA792_ASAP51_ctrl_NP19-36_SN_1"  "AA_ASAP137_PD_NP23-21_SN_1"     
##   [5] "DA487_ASAP8_ctrl_PT231_SN_1"     "DA479_ASAP7_ctrl_NP16-21_SN_2"  
##   [7] "DA433_ASAP5_ctrl_NP16-161_SN_2"  "DA431_ASAP4_PD_P74_SN_2"        
##   [9] "DA784_ASAP46_ctrl_NP17-256_SN_2" "DA475_ASAP2_PD_NP16-25_SN_2"    
##  [11] "AA_ASAP129_ctrl_NP22-37_SN_2"    "AA_ASAP118_PD_NP22-55_SN_2"     
##  [13] "AA_ASAP99_ctrl_NP16-284_SN_2"    "DA782_ASAP41_PD_NP19-108_SN_2"  
##  [15] "AA_ASAP133_PD_NP17-232_SN_2"     "AA_ASAP132_PD_NP16-285_SN_2"    
##  [17] "DA796_ASAP57_ctrl_NP19-45_SN_2"  "AA_ASAP137_PD_NP23-21_SN_2"     
##  [19] "DA794_ASAP54_ctrl_NP19-37_SN_2"  "DA792_ASAP51_ctrl_NP19-36_SN_2" 
##  [21] "AA_ASAP101_PD_NP21-57_SN_2"      "DA489_ASAP3_PD_P73_SN_2"        
##  [23] "AA_ASAP103_PD_NP21-217_SN_2"     "AA_ASAP102_PD_NP21-208_SN_2"    
##  [25] "DA511_ASAP21_PD_NP16-269_SN_2"   "MJ_ASAP6_ctrl_NP16-164_SN_2"    
##  [27] "AA_ASAP104_ctrl_NP16-119_SN_2"   "DA429_ASAP1_PD_NP16-162_SN_2"   
##  [29] "AA_ASAP135_PD_NP19-137_SN_2"     "DA487_ASAP8_ctrl_PT231_SN_2"    
##  [31] "AA_ASAP127_ctrl_NP19-218_SN_2"   "AA_ASAP108_ctrl_NP18-148_SN_2"  
##  [33] "AA_ASAP134_PD_NP19-91_SN_2"      "DA473_ASAP38_PD_NP19-23_SN_2"   
##  [35] "AA_ASAP105_ctrl_NP16-293_SN_2"   "AA_ASAP132_PD_NP16-285_SN_3"    
##  [37] "AA_ASAP133_PD_NP17-232_SN_3"     "DA796_ASAP57_ctrl_NP19-45_SN_3" 
##  [39] "AA_ASAP103_PD_NP21-217_SN_3"     "DA511_ASAP21_PD_NP16-269_SN_3"  
##  [41] "AA_ASAP101_PD_NP21-57_SN_3"      "AA_ASAP102_PD_NP21-208_SN_3"    
##  [43] "DA473_ASAP38_PD_NP19-23_SN_3"    "AA_ASAP105_ctrl_NP16-293_SN_3"  
##  [45] "AA_ASAP108_ctrl_NP18-148_SN_3"   "DA794_ASAP54_ctrl_NP19-37_SN_3" 
##  [47] "DA792_ASAP51_ctrl_NP19-36_SN_3"  "DA431_ASAP4_PD_P74_SN_3"        
##  [49] "AA_ASAP127_ctrl_NP19-218_SN_3"   "AA_ASAP136_PD_NP21-04_SN_3"     
##  [51] "MJ_ASAP6_ctrl_NP16-164_SN_3"     "DA479_ASAP7_ctrl_NP16-21_SN_3"  
##  [53] "DA475_ASAP2_PD_NP16-25_SN_3"     "DA433_ASAP5_ctrl_NP16-161_SN_3" 
##  [55] "AA_ASAP129_ctrl_NP22-37_SN_3"    "DA489_ASAP3_PD_P73_SN_3"        
##  [57] "AA_ASAP137_PD_NP23-21_SN_3"      "AA_ASAP135_PD_NP19-137_SN_3"    
##  [59] "DA487_ASAP8_ctrl_PT231_SN_3"     "AA_ASAP99_ctrl_NP16-284_SN_3"   
##  [61] "DA429_ASAP1_PD_NP16-162_SN_3"    "AA_ASAP134_PD_NP19-91_SN_3"     
##  [63] "AA_ASAP118_PD_NP22-55_SN_3"      "DA784_ASAP46_ctrl_NP17-256_SN_3"
##  [65] "AA_ASAP104_ctrl_NP16-119_SN_3"   "DA782_ASAP41_PD_NP19-108_SN_3"  
##  [67] "AA_ASAP136_PD_NP21-04_SN_5"      "DA431_ASAP4_PD_P74_SN_5"        
##  [69] "AA_ASAP129_ctrl_NP22-37_SN_5"    "AA_ASAP127_ctrl_NP19-218_SN_5"  
##  [71] "MJ_ASAP6_ctrl_NP16-164_SN_5"     "DA473_ASAP38_PD_NP19-23_SN_5"   
##  [73] "AA_ASAP108_ctrl_NP18-148_SN_5"   "AA_ASAP132_PD_NP16-285_SN_5"    
##  [75] "DA487_ASAP8_ctrl_PT231_SN_5"     "DA792_ASAP51_ctrl_NP19-36_SN_5" 
##  [77] "DA782_ASAP41_PD_NP19-108_SN_5"   "DA479_ASAP7_ctrl_NP16-21_SN_5"  
##  [79] "DA796_ASAP57_ctrl_NP19-45_SN_5"  "DA784_ASAP46_ctrl_NP17-256_SN_5"
##  [81] "AA_ASAP99_ctrl_NP16-284_SN_5"    "AA_ASAP105_ctrl_NP16-293_SN_5"  
##  [83] "DA429_ASAP1_PD_NP16-162_SN_5"    "AA_ASAP137_PD_NP23-21_SN_5"     
##  [85] "AA_ASAP101_PD_NP21-57_SN_5"      "AA_ASAP103_PD_NP21-217_SN_5"    
##  [87] "DA489_ASAP3_PD_P73_SN_5"         "DA511_ASAP21_PD_NP16-269_SN_5"  
##  [89] "DA475_ASAP2_PD_NP16-25_SN_5"     "AA_ASAP135_PD_NP19-137_SN_5"    
##  [91] "AA_ASAP104_ctrl_NP16-119_SN_5"   "DA433_ASAP5_ctrl_NP16-161_SN_5" 
##  [93] "AA_ASAP102_PD_NP21-208_SN_5"     "DA794_ASAP54_ctrl_NP19-37_SN_5" 
##  [95] "AA_ASAP118_PD_NP22-55_SN_5"      "AA_ASAP133_PD_NP17-232_SN_5"    
##  [97] "AA_ASAP134_PD_NP19-91_SN_5"      "AA_ASAP134_PD_NP19-91_SN_4"     
##  [99] "DA431_ASAP4_PD_P74_SN_4"         "DA487_ASAP8_ctrl_PT231_SN_4"    
## [101] "DA473_ASAP38_PD_NP19-23_SN_4"    "AA_ASAP129_ctrl_NP22-37_SN_4"   
## [103] "AA_ASAP108_ctrl_NP18-148_SN_4"   "AA_ASAP137_PD_NP23-21_SN_4"     
## [105] "AA_ASAP102_PD_NP21-208_SN_4"     "AA_ASAP104_ctrl_NP16-119_SN_4"  
## [107] "AA_ASAP127_ctrl_NP19-218_SN_4"   "AA_ASAP101_PD_NP21-57_SN_4"     
## [109] "AA_ASAP103_PD_NP21-217_SN_4"     "DA489_ASAP3_PD_P73_SN_4"        
## [111] "DA511_ASAP21_PD_NP16-269_SN_4"   "MJ_ASAP6_ctrl_NP16-164_SN_4"    
## [113] "DA782_ASAP41_PD_NP19-108_SN_4"   "AA_ASAP118_PD_NP22-55_SN_4"     
## [115] "DA429_ASAP1_PD_NP16-162_SN_4"    "DA792_ASAP51_ctrl_NP19-36_SN_4" 
## [117] "AA_ASAP133_PD_NP17-232_SN_4"     "AA_ASAP135_PD_NP19-137_SN_4"    
## [119] "DA433_ASAP5_ctrl_NP16-161_SN_4"  "DA475_ASAP2_PD_NP16-25_SN_4"    
## [121] "DA794_ASAP54_ctrl_NP19-37_SN_4" 
## 
## $order_rows
##    [1] "HERV_dup277"    "HERV_dup38"     "HERV_dup183"    "HERV_dup2278"  
##    [5] "HERV_dup909"    "HERV_dup276"    "HERV_dup3033"   "HERV_dup1243"  
##    [9] "HERV_dup1731"   "HERV_dup1236"   "HERV_dup2607"   "HERV_dup54"    
##   [13] "HERV_dup670"    "HERV_dup671"    "HERV_dup1437"   "HERV_dup1778"  
##   [17] "HERV_dup2524"   "HERV_dup3118"   "HERV_dup2631"   "HERV_dup417"   
##   [21] "HERV_dup2772"   "HERV_dup1638"   "HERV_dup184"    "HERV_dup1661"  
##   [25] "HERV_dup2942"   "HERV_dup2967"   "HERV_dup471"    "HERV_dup2290"  
##   [29] "HERV_dup1201"   "HERV_dup916"    "HERV_dup2383"   "HERV_dup194"   
##   [33] "HERV_dup2834"   "HERV_dup1658"   "HERV_dup1662"   "HERV_dup1433"  
##   [37] "HERV_dup975"    "HERV_dup724"    "HERV_dup1413"   "HERV_dup1381"  
##   [41] "HERV_dup1304"   "HERV_dup1605"   "HERV_dup1926"   "HERV_dup2391"  
##   [45] "HERV_dup846"    "HERV_dup409"    "HERV_dup2801"   "HERV_dup27"    
##   [49] "HERV_dup243"    "HERV_dup2480"   "HERV_dup1470"   "HERV_dup2733"  
##   [53] "HERV_dup3100"   "HERV_dup3239"   "HERV_dup882"    "HERV_dup703"   
##   [57] "HERV_dup3270"   "HERV_dup3171"   "HERV_dup662"    "HERV_dup2555"  
##   [61] "HERV_dup2530"   "HERV_dup1383"   "HERV_dup1195"   "HERV_dup1285"  
##   [65] "HERV_dup1081"   "HERV_dup1891"   "HERV_dup1416"   "HERV_dup851"   
##   [69] "HERV_dup1082"   "HERV_dup899"    "HERV_dup3358"   "HERV_dup1953"  
##   [73] "HERV_dup1587"   "HERV_dup1526"   "HERV_dup1184"   "HERV_dup2635"  
##   [77] "HERV_dup1222"   "HERV_dup2797"   "HERV_dup599"    "HERV_dup433"   
##   [81] "HERV_dup3187"   "HERV_dup407"    "HERV_dup2603"   "HERV_dup389"   
##   [85] "HERV_dup2604"   "HERV_dup1156"   "HERV_dup2778"   "HERV_dup3335"  
##   [89] "HERV_dup1268"   "HERV_dup118"    "HERV_dup573"    "HERV_dup1245"  
##   [93] "HERV_dup127"    "HERV_dup1804"   "HERV_dup2149"   "HERV_dup2529"  
##   [97] "HERV_dup1108"   "HERV_dup1005"   "HERV_dup2378"   "HERV_dup2907"  
##  [101] "HERV_dup728"    "HERV_dup736"    "HERV_dup577"    "HERV_dup1979"  
##  [105] "HERV_dup2264"   "HERV_dup2356"   "HERV_dup870"    "HERV_dup2804"  
##  [109] "HERV_dup1071"   "HERV_dup331"    "HERV_dup935"    "HERV_dup1972"  
##  [113] "HERV_dup1327"   "HERV_dup1656"   "HERV_dup2566"   "HERV_dup1532"  
##  [117] "HERV_dup3154"   "HERV_dup2972"   "HERV_dup356"    "HERV_dup2548"  
##  [121] "HERV_dup692"    "HERV_dup2130"   "HERV_dup2100"   "HERV_dup517"   
##  [125] "HERV_dup3694"   "HERV_dup2353"   "HERV_dup487"    "HERV_dup3519"  
##  [129] "HERV_dup355"    "HERV_dup3394"   "HERV_dup3286"   "HERV_dup1316"  
##  [133] "HERV_dup1307"   "HERV_dup1401"   "HERV_dup2632"   "HERV_dup894"   
##  [137] "HERV_dup3406"   "HERV_dup3131"   "HERV_dup508"    "HERV_dup1036"  
##  [141] "HERV_dup665"    "HERV_dup1491"   "HERV_dup419"    "HERV_dup591"   
##  [145] "HERV_dup2320"   "HERV_dup2843"   "HERV_dup2183"   "HERV_dup572"   
##  [149] "HERV_dup977"    "HERV_dup185"    "HERV_dup1208"   "HERV_dup1253"  
##  [153] "HERV_dup1556"   "HERV_dup201"    "HERV_dup2647"   "HERV_dup1378"  
##  [157] "HERV_dup1073"   "HERV_dup2324"   "HERV_dup441"    "HERV_dup3182"  
##  [161] "HERV_dup3606"   "HERV_dup446"    "HERV_dup115"    "HERV_dup2941"  
##  [165] "HERV_dup3189"   "HERV_dup3015"   "HERV_dup1752"   "HERV_dup2242"  
##  [169] "HERV_dup3284"   "HERV_dup2878"   "HERV_dup388"    "HERV_dup1093"  
##  [173] "HERV_dup2735"   "HERV_dup1047"   "HERV_dup1017"   "HERV_dup1733"  
##  [177] "HERV_dup981"    "HERV_dup3210"   "HERV_dup3037"   "HERV_dup2646"  
##  [181] "HERV_dup1668"   "HERV_dup1730"   "HERV_dup3143"   "HERV_dup746"   
##  [185] "HERV_dup2936"   "HERV_dup1440"   "HERV_dup772"    "HERV_dup735"   
##  [189] "HERV_dup530"    "HERV_dup250"    "HERV_dup1520"   "HERV_dup2949"  
##  [193] "HERV_dup1933"   "HERV_dup1932"   "HERV_dup966"    "HERV_dup1667"  
##  [197] "HERV_dup1948"   "HERV_dup398"    "HERV_dup369"    "HERV_dup554"   
##  [201] "HERV_dup1389"   "HERV_dup2857"   "HERV_dup1350"   "HERV_dup120"   
##  [205] "HERV_dup381"    "HERV_dup1366"   "HERV_dup133"    "HERV_dup3179"  
##  [209] "HERV_dup2187"   "HERV_dup3013"   "HERV_dup3031"   "HERV_dup1210"  
##  [213] "HERV_dup1302"   "HERV_dup1248"   "HERV_dup2663"   "HERV_dup634"   
##  [217] "HERV_dup1046"   "HERV_dup1962"   "HERV_dup551"    "HERV_dup3044"  
##  [221] "HERV_dup1187"   "HERV_dup2152"   "HERV_dup1557"   "HERV_dup2879"  
##  [225] "HERV_dup1228"   "HERV_dup177"    "HERV_dup1412"   "HERV_dup2939"  
##  [229] "HERV_dup152"    "HERV_dup1112"   "HERV_dup180"    "HERV_dup1212"  
##  [233] "HERV_dup3108"   "HERV_dup2141"   "HERV_dup1213"   "HERV_dup565"   
##  [237] "HERV_dup850"    "HERV_dup3016"   "HERV_dup2823"   "HERV_dup1869"  
##  [241] "HERV_dup2464"   "HERV_dup3215"   "HERV_dup1757"   "HERV_dup2481"  
##  [245] "HERV_dup586"    "HERV_dup3408"   "HERV_dup357"    "HERV_dup2518"  
##  [249] "HERV_dup739"    "HERV_dup443"    "HERV_dup1823"   "HERV_dup3607"  
##  [253] "HERV_dup2217"   "HERV_dup509"    "HERV_dup2655"   "HERV_dup3212"  
##  [257] "HERV_dup2894"   "HERV_dup1500"   "HERV_dup450"    "HERV_dup29"    
##  [261] "HERV_dup1724"   "HERV_dup3319"   "HERV_dup1239"   "HERV_dup3430"  
##  [265] "HERV_dup3481"   "HERV_dup314"    "HERV_dup613"    "HERV_dup884"   
##  [269] "HERV_dup39"     "HERV_dup1629"   "HERV_dup1295"   "HERV_dup2557"  
##  [273] "HERV_dup2129"   "HERV_dup1453"   "HERV_dup1218"   "HERV_dup1958"  
##  [277] "HERV_dup1049"   "HERV_dup2706"   "HERV_dup1003"   "HERV_dup1851"  
##  [281] "HERV_dup2441"   "HERV_dup1931"   "HERV_dup321"    "HERV_dup3219"  
##  [285] "HERV_dup1459"   "HERV_dup3137"   "HERV_dup1131"   "HERV_dup3063"  
##  [289] "HERV_dup930"    "HERV_dup2620"   "HERV_dup2886"   "HERV_dup3073"  
##  [293] "HERV_dup570"    "HERV_dup1415"   "HERV_dup982"    "HERV_dup2680"  
##  [297] "HERV_dup492"    "HERV_dup86"     "HERV_dup2192"   "HERV_dup1639"  
##  [301] "HERV_dup2747"   "HERV_dup23"     "HERV_dup732"    "HERV_dup682"   
##  [305] "HERV_dup710"    "HERV_dup1934"   "HERV_dup2602"   "HERV_dup1374"  
##  [309] "HERV_dup1403"   "HERV_dup293"    "HERV_dup568"    "HERV_dup578"   
##  [313] "HERV_dup2875"   "HERV_dup400"    "HERV_dup2728"   "HERV_dup17"    
##  [317] "HERV_dup1438"   "HERV_dup348"    "HERV_dup2809"   "HERV_dup3248"  
##  [321] "HERV_dup2034"   "HERV_dup2415"   "HERV_dup399"    "HERV_dup3505"  
##  [325] "HERV_dup1640"   "HERV_dup1089"   "HERV_dup2303"   "HERV_dup3588"  
##  [329] "HERV_dup1943"   "HERV_dup3507"   "HERV_dup1278"   "HERV_dup2561"  
##  [333] "HERV_dup831"    "HERV_dup1513"   "HERV_dup2945"   "HERV_dup1514"  
##  [337] "HERV_dup3181"   "HERV_dup1242"   "HERV_dup729"    "HERV_dup1579"  
##  [341] "HERV_dup469"    "HERV_dup3217"   "HERV_dup1272"   "HERV_dup2653"  
##  [345] "HERV_dup21"     "HERV_dup84"     "HERV_dup3673"   "HERV_dup1331"  
##  [349] "HERV_dup1279"   "HERV_dup3008"   "HERV_dup57"     "HERV_dup1099"  
##  [353] "HERV_dup803"    "HERV_dup1653"   "HERV_dup1920"   "HERV_dup1720"  
##  [357] "HERV_dup2905"   "HERV_dup1356"   "HERV_dup2536"   "HERV_dup2128"  
##  [361] "HERV_dup2840"   "HERV_dup2977"   "HERV_dup251"    "HERV_dup3363"  
##  [365] "HERV_dup2159"   "HERV_dup1303"   "HERV_dup2743"   "HERV_dup5"     
##  [369] "HERV_dup350"    "HERV_dup2562"   "HERV_dup2937"   "HERV_dup2533"  
##  [373] "HERV_dup3366"   "HERV_dup773"    "HERV_dup1321"   "HERV_dup1613"  
##  [377] "HERV_dup1914"   "HERV_dup890"    "HERV_dup1351"   "HERV_dup36"    
##  [381] "HERV_dup2963"   "HERV_dup949"    "HERV_dup1203"   "HERV_dup3388"  
##  [385] "HERV_dup2900"   "HERV_dup1569"   "HERV_dup3231"   "HERV_dup214"   
##  [389] "HERV_dup1512"   "HERV_dup1875"   "HERV_dup2855"   "HERV_dup151"   
##  [393] "HERV_dup2848"   "HERV_dup1417"   "HERV_dup1890"   "HERV_dup913"   
##  [397] "HERV_dup3580"   "HERV_dup3522"   "HERV_dup3220"   "HERV_dup2812"  
##  [401] "HERV_dup34"     "HERV_dup2550"   "HERV_dup1090"   "HERV_dup26"    
##  [405] "HERV_dup3287"   "HERV_dup94"     "HERV_dup129"    "HERV_dup1371"  
##  [409] "HERV_dup2179"   "HERV_dup1847"   "HERV_dup1001"   "HERV_dup1846"  
##  [413] "HERV_dup990"    "HERV_dup2891"   "HERV_dup1298"   "HERV_dup2599"  
##  [417] "HERV_dup1334"   "HERV_dup1269"   "HERV_dup2736"   "HERV_dup1755"  
##  [421] "HERV_dup2785"   "HERV_dup2027"   "HERV_dup386"    "HERV_dup1717"  
##  [425] "HERV_dup2166"   "HERV_dup112"    "HERV_dup1050"   "HERV_dup1339"  
##  [429] "HERV_dup3148"   "HERV_dup2334"   "HERV_dup632"    "HERV_dup1611"  
##  [433] "HERV_dup758"    "HERV_dup799"    "HERV_dup301"    "HERV_dup2002"  
##  [437] "HERV_dup1750"   "HERV_dup3105"   "HERV_dup2964"   "HERV_dup2319"  
##  [441] "HERV_dup1052"   "HERV_dup1029"   "HERV_dup1614"   "HERV_dup933"   
##  [445] "HERV_dup2436"   "HERV_dup3050"   "HERV_dup488"    "HERV_dup776"   
##  [449] "HERV_dup344"    "HERV_dup203"    "HERV_dup1107"   "HERV_dup1935"  
##  [453] "HERV_dup1390"   "HERV_dup1364"   "HERV_dup2033"   "HERV_dup1346"  
##  [457] "HERV_dup110"    "HERV_dup723"    "HERV_dup1868"   "HERV_dup2897"  
##  [461] "HERV_dup58"     "HERV_dup968"    "HERV_dup108"    "HERV_dup3117"  
##  [465] "HERV_dup1324"   "HERV_dup3328"   "HERV_dup3416"   "HERV_dup3140"  
##  [469] "HERV_dup2250"   "HERV_dup2163"   "HERV_dup852"    "HERV_dup2500"  
##  [473] "HERV_dup2235"   "HERV_dup873"    "HERV_dup482"    "HERV_dup2273"  
##  [477] "HERV_dup1345"   "HERV_dup2188"   "HERV_dup3124"   "HERV_dup1080"  
##  [481] "HERV_dup1447"   "HERV_dup2041"   "HERV_dup3341"   "HERV_dup626"   
##  [485] "HERV_dup3459"   "HERV_dup1780"   "HERV_dup2934"   "HERV_dup2112"  
##  [489] "HERV_dup3251"   "HERV_dup3107"   "HERV_dup329"    "HERV_dup434"   
##  [493] "HERV_dup2896"   "HERV_dup640"    "HERV_dup1617"   "HERV_dup934"   
##  [497] "HERV_dup1719"   "HERV_dup377"    "HERV_dup1707"   "HERV_dup1541"  
##  [501] "HERV_dup1240"   "HERV_dup597"    "HERV_dup3351"   "HERV_dup904"   
##  [505] "HERV_dup2282"   "HERV_dup1923"   "HERV_dup2476"   "HERV_dup900"   
##  [509] "HERV_dup1333"   "HERV_dup2422"   "HERV_dup2379"   "HERV_dup1655"  
##  [513] "HERV_dup956"    "HERV_dup1235"   "HERV_dup65"     "HERV_dup1598"  
##  [517] "HERV_dup2739"   "HERV_dup3020"   "HERV_dup18"     "HERV_dup1449"  
##  [521] "HERV_dup3355"   "HERV_dup1319"   "HERV_dup1322"   "HERV_dup2019"  
##  [525] "HERV_dup1657"   "HERV_dup202"    "HERV_dup2847"   "HERV_dup2525"  
##  [529] "HERV_dup282"    "HERV_dup218"    "HERV_dup1007"   "HERV_dup467"   
##  [533] "HERV_dup2366"   "HERV_dup272"    "HERV_dup2404"   "HERV_dup2093"  
##  [537] "HERV_dup2298"   "HERV_dup1663"   "HERV_dup777"    "HERV_dup2784"  
##  [541] "HERV_dup2292"   "HERV_dup2365"   "HERV_dup562"    "HERV_dup1362"  
##  [545] "HERV_dup1359"   "HERV_dup3198"   "HERV_dup1596"   "HERV_dup1802"  
##  [549] "HERV_dup2111"   "HERV_dup2261"   "HERV_dup2176"   "HERV_dup1282"  
##  [553] "HERV_dup1703"   "HERV_dup380"    "HERV_dup292"    "HERV_dup1102"  
##  [557] "HERV_dup1004"   "HERV_dup2266"   "HERV_dup1694"   "HERV_dup3266"  
##  [561] "HERV_dup2769"   "HERV_dup939"    "HERV_dup1382"   "HERV_dup612"   
##  [565] "HERV_dup468"    "HERV_dup470"    "HERV_dup1670"   "HERV_dup1982"  
##  [569] "HERV_dup1315"   "HERV_dup1917"   "HERV_dup1702"   "HERV_dup1671"  
##  [573] "HERV_dup290"    "HERV_dup1888"   "HERV_dup2803"   "HERV_dup2598"  
##  [577] "HERV_dup2106"   "HERV_dup2623"   "HERV_dup2915"   "HERV_dup2966"  
##  [581] "HERV_dup2877"   "HERV_dup249"    "HERV_dup2182"   "HERV_dup2012"  
##  [585] "HERV_dup3410"   "HERV_dup1209"   "HERV_dup2856"   "HERV_dup1973"  
##  [589] "HERV_dup2438"   "HERV_dup1484"   "HERV_dup2914"   "HERV_dup1357"  
##  [593] "HERV_dup872"    "HERV_dup1002"   "HERV_dup954"    "HERV_dup600"   
##  [597] "HERV_dup2412"   "HERV_dup927"    "HERV_dup2961"   "HERV_dup3390"  
##  [601] "HERV_dup1283"   "HERV_dup1308"   "HERV_dup3417"   "HERV_dup1297"  
##  [605] "HERV_dup2085"   "HERV_dup384"    "HERV_dup1317"   "HERV_dup3365"  
##  [609] "HERV_dup2651"   "HERV_dup2962"   "HERV_dup1281"   "HERV_dup1048"  
##  [613] "HERV_dup1114"   "HERV_dup2985"   "HERV_dup300"    "HERV_dup1394"  
##  [617] "HERV_dup1255"   "HERV_dup209"    "HERV_dup3226"   "HERV_dup969"   
##  [621] "HERV_dup2158"   "HERV_dup1756"   "HERV_dup926"    "HERV_dup3342"  
##  [625] "HERV_dup3343"   "HERV_dup2376"   "HERV_dup2589"   "HERV_dup2588"  
##  [629] "HERV_dup93"     "HERV_dup980"    "HERV_dup474"    "HERV_dup3529"  
##  [633] "HERV_dup2695"   "HERV_dup1940"   "HERV_dup2789"   "HERV_dup2299"  
##  [637] "HERV_dup2134"   "HERV_dup61"     "HERV_dup880"    "HERV_dup2643"  
##  [641] "HERV_dup1358"   "HERV_dup1"      "HERV_dup37"     "HERV_dup1889"  
##  [645] "HERV_dup717"    "HERV_dup288"    "HERV_dup2841"   "HERV_dup1000"  
##  [649] "HERV_dup1669"   "HERV_dup1701"   "HERV_dup302"    "HERV_dup3375"  
##  [653] "HERV_dup731"    "HERV_dup1758"   "HERV_dup3423"   "HERV_dup2662"  
##  [657] "HERV_dup2491"   "HERV_dup265"    "HERV_dup1456"   "HERV_dup1232"  
##  [661] "HERV_dup1310"   "HERV_dup3379"   "HERV_dup1309"   "HERV_dup518"   
##  [665] "HERV_dup3418"   "HERV_dup1708"   "HERV_dup1079"   "HERV_dup3252"  
##  [669] "HERV_dup3174"   "HERV_dup2752"   "HERV_dup3357"   "HERV_dup379"   
##  [673] "HERV_dup2381"   "HERV_dup2838"   "HERV_dup2880"   "HERV_dup940"   
##  [677] "HERV_dup614"    "HERV_dup979"    "HERV_dup2902"   "HERV_dup1749"  
##  [681] "L1PA3_dup7792"  "L1PA3_dup5047"  "L1PA3_dup2662"  "L1PA3_dup2683" 
##  [685] "L1PA2_dup741"   "L1PA3_dup4408"  "L1PA2_dup2496"  "L1PA2_dup994"  
##  [689] "L1PA2_dup4651"  "L1PA3_dup8328"  "L1PA2_dup39"    "L1PA3_dup1264" 
##  [693] "L1PA3_dup9734"  "L1PA3_dup6160"  "L1HS_dup831"    "L1PA3_dup4688" 
##  [697] "L1PA3_dup9473"  "L1PA3_dup6112"  "L1PA3_dup4487"  "L1PA2_dup3881" 
##  [701] "L1PA3_dup9255"  "L1PA2_dup4596"  "L1PA2_dup3405"  "L1HS_dup916"   
##  [705] "L1PA3_dup5057"  "L1PA2_dup2271"  "L1PA3_dup1988"  "L1PA3_dup6584" 
##  [709] "L1PA2_dup4775"  "L1PA2_dup3607"  "L1PA3_dup3306"  "L1PA2_dup559"  
##  [713] "L1PA3_dup2039"  "L1PA2_dup4367"  "L1PA3_dup1952"  "L1PA3_dup2954" 
##  [717] "L1PA3_dup9430"  "L1PA3_dup10344" "L1PA3_dup4884"  "L1PA2_dup326"  
##  [721] "L1PA3_dup1723"  "L1PA3_dup128"   "L1PA2_dup4618"  "L1PA2_dup1746" 
##  [725] "L1HS_dup379"    "L1PA2_dup2343"  "L1PA3_dup5510"  "L1PA2_dup2430" 
##  [729] "L1PA3_dup3502"  "L1PA3_dup7432"  "L1PA3_dup5418"  "L1HS_dup155"   
##  [733] "L1PA2_dup1760"  "L1PA2_dup2581"  "L1PA2_dup2863"  "L1PA3_dup5238" 
##  [737] "L1PA2_dup1653"  "L1PA2_dup413"   "L1PA3_dup8173"  "L1PA3_dup6317" 
##  [741] "L1PA3_dup9840"  "L1PA3_dup8891"  "L1HS_dup270"    "L1PA2_dup589"  
##  [745] "L1PA3_dup10525" "L1PA3_dup8506"  "L1PA2_dup423"   "L1PA2_dup98"   
##  [749] "L1PA2_dup3484"  "L1PA3_dup10096" "L1HS_dup376"    "L1PA3_dup5355" 
##  [753] "L1PA3_dup5358"  "L1PA3_dup5540"  "L1PA2_dup4776"  "L1PA3_dup2643" 
##  [757] "L1PA3_dup1547"  "L1PA3_dup3954"  "L1PA3_dup2357"  "L1PA3_dup3300" 
##  [761] "L1PA2_dup4309"  "L1HS_dup907"    "L1PA2_dup1560"  "L1PA3_dup5468" 
##  [765] "L1PA2_dup1058"  "L1PA3_dup1428"  "L1PA3_dup7316"  "L1HS_dup62"    
##  [769] "L1PA3_dup4668"  "L1PA3_dup1554"  "L1PA3_dup3509"  "L1PA3_dup5745" 
##  [773] "L1PA2_dup4226"  "L1PA2_dup3622"  "L1PA2_dup3445"  "L1PA3_dup1528" 
##  [777] "L1PA2_dup16"    "L1PA3_dup6966"  "L1PA3_dup5928"  "L1PA2_dup747"  
##  [781] "L1PA2_dup1248"  "L1PA3_dup6436"  "L1PA3_dup6008"  "L1HS_dup405"   
##  [785] "L1PA3_dup2204"  "L1PA2_dup4053"  "L1PA2_dup3503"  "L1PA2_dup4901" 
##  [789] "L1HS_dup679"    "L1HS_dup1286"   "L1HS_dup1324"   "L1HS_dup90"    
##  [793] "L1HS_dup1295"   "L1PA3_dup8896"  "L1PA3_dup6730"  "L1PA3_dup3102" 
##  [797] "L1PA2_dup3042"  "L1PA2_dup3283"  "L1PA2_dup4045"  "L1PA3_dup1027" 
##  [801] "L1PA3_dup1026"  "L1PA2_dup1331"  "L1PA3_dup3729"  "L1PA2_dup1978" 
##  [805] "L1PA2_dup684"   "L1PA2_dup2168"  "L1PA3_dup6871"  "L1PA3_dup6523" 
##  [809] "L1HS_dup225"    "L1PA3_dup1770"  "L1HS_dup1014"   "L1PA2_dup4522" 
##  [813] "L1PA2_dup4639"  "L1PA2_dup4441"  "L1HS_dup803"    "L1PA2_dup1476" 
##  [817] "L1HS_dup1514"   "L1PA2_dup4389"  "L1PA2_dup798"   "L1PA2_dup1177" 
##  [821] "L1PA2_dup109"   "L1PA3_dup9866"  "L1PA2_dup1398"  "L1PA2_dup3426" 
##  [825] "L1HS_dup1437"   "L1PA3_dup2620"  "L1PA3_dup3484"  "L1PA3_dup3291" 
##  [829] "L1PA3_dup1337"  "L1PA2_dup3160"  "L1PA2_dup4548"  "L1PA2_dup2047" 
##  [833] "L1PA3_dup3684"  "L1HS_dup1342"   "L1PA2_dup1463"  "L1PA3_dup1463" 
##  [837] "L1PA2_dup4478"  "L1HS_dup1616"   "L1HS_dup1393"   "L1PA2_dup2180" 
##  [841] "L1PA2_dup805"   "L1PA2_dup4611"  "L1PA2_dup3629"  "L1PA2_dup2537" 
##  [845] "L1HS_dup444"    "L1HS_dup1491"   "L1HS_dup1284"   "L1PA3_dup4393" 
##  [849] "L1HS_dup1501"   "L1PA2_dup472"   "L1PA2_dup2004"  "L1PA3_dup683"  
##  [853] "L1HS_dup143"    "L1PA2_dup4713"  "L1PA2_dup382"   "L1HS_dup429"   
##  [857] "L1HS_dup163"    "L1HS_dup204"    "L1PA2_dup4432"  "L1PA2_dup1049" 
##  [861] "L1HS_dup802"    "L1PA2_dup2444"  "L1PA2_dup3118"  "L1PA2_dup4612" 
##  [865] "L1PA3_dup3959"  "L1PA2_dup2436"  "L1PA3_dup7288"  "L1HS_dup370"   
##  [869] "L1PA2_dup4335"  "L1PA2_dup2504"  "L1PA2_dup4652"  "L1PA3_dup8117" 
##  [873] "L1PA3_dup840"   "L1PA3_dup3404"  "L1PA3_dup5363"  "L1PA2_dup2506" 
##  [877] "L1PA2_dup2261"  "L1HS_dup600"    "L1PA2_dup3766"  "L1PA3_dup5825" 
##  [881] "L1PA3_dup1727"  "L1PA3_dup1943"  "L1PA3_dup10072" "L1PA3_dup638"  
##  [885] "L1HS_dup466"    "L1HS_dup1104"   "L1PA2_dup2577"  "L1PA2_dup360"  
##  [889] "L1PA2_dup4378"  "L1PA2_dup759"   "L1HS_dup1077"   "L1PA2_dup726"  
##  [893] "L1HS_dup811"    "L1HS_dup579"    "L1PA2_dup3776"  "L1PA3_dup1989" 
##  [897] "L1PA3_dup5544"  "L1PA2_dup3292"  "L1HS_dup1357"   "L1PA2_dup4043" 
##  [901] "L1PA2_dup2282"  "L1PA3_dup7893"  "L1PA3_dup345"   "L1PA2_dup514"  
##  [905] "L1PA3_dup3005"  "L1HS_dup995"    "L1PA2_dup1621"  "L1PA3_dup8310" 
##  [909] "L1PA2_dup4421"  "L1PA3_dup8313"  "L1PA2_dup2385"  "L1PA2_dup1968" 
##  [913] "L1PA2_dup383"   "L1PA2_dup4201"  "L1PA2_dup935"   "L1PA3_dup2389" 
##  [917] "L1PA2_dup2295"  "L1HS_dup35"     "L1PA3_dup5866"  "L1PA3_dup9373" 
##  [921] "L1PA2_dup2729"  "L1HS_dup1478"   "L1PA3_dup3586"  "L1PA2_dup3003" 
##  [925] "L1PA3_dup10176" "L1PA3_dup3153"  "L1PA2_dup3930"  "L1PA3_dup3763" 
##  [929] "L1PA2_dup4262"  "L1PA3_dup10043" "L1PA3_dup5207"  "L1PA2_dup358"  
##  [933] "L1PA2_dup4688"  "L1PA2_dup678"   "L1PA2_dup1023"  "L1PA2_dup4237" 
##  [937] "L1PA2_dup365"   "L1PA2_dup4686"  "L1HS_dup1576"   "L1PA2_dup2254" 
##  [941] "L1PA2_dup4762"  "L1PA2_dup675"   "L1PA3_dup1550"  "L1PA3_dup4596" 
##  [945] "L1PA3_dup10011" "L1PA3_dup9856"  "L1HS_dup111"    "L1HS_dup1243"  
##  [949] "L1PA2_dup2876"  "L1PA2_dup4791"  "L1HS_dup1473"   "L1PA3_dup9722" 
##  [953] "L1PA2_dup949"   "L1PA2_dup3439"  "L1PA3_dup9702"  "L1PA2_dup307"  
##  [957] "L1PA2_dup4936"  "L1HS_dup622"    "L1HS_dup1339"   "L1HS_dup87"    
##  [961] "L1PA3_dup247"   "L1PA3_dup4603"  "L1PA3_dup3323"  "L1PA2_dup4430" 
##  [965] "L1PA3_dup3950"  "L1HS_dup124"    "L1PA2_dup3773"  "L1PA2_dup219"  
##  [969] "L1PA2_dup4454"  "L1PA2_dup1490"  "L1HS_dup1020"   "L1PA3_dup5886" 
##  [973] "L1PA3_dup5106"  "L1PA2_dup629"   "L1HS_dup1005"   "L1PA2_dup1426" 
##  [977] "L1PA2_dup1050"  "L1PA2_dup4196"  "L1PA3_dup10531" "L1PA3_dup6387" 
##  [981] "L1PA3_dup5594"  "L1HS_dup743"    "L1PA2_dup2408"  "L1PA3_dup7605" 
##  [985] "L1PA2_dup2089"  "L1HS_dup649"    "L1PA3_dup5927"  "L1PA3_dup6884" 
##  [989] "L1HS_dup879"    "L1PA3_dup2755"  "L1PA2_dup1112"  "L1PA3_dup7947" 
##  [993] "L1PA3_dup1328"  "L1PA3_dup3863"  "L1HS_dup1019"   "L1PA3_dup1046" 
##  [997] "L1PA2_dup3425"  "L1PA2_dup732"   "L1PA2_dup1992"  "L1PA2_dup2127" 
## [1001] "L1PA2_dup4528"  "L1HS_dup787"    "L1PA3_dup9202"  "L1PA2_dup2565" 
## [1005] "L1HS_dup244"    "L1PA3_dup1647"  "L1PA2_dup1078"  "L1PA3_dup9946" 
## [1009] "L1PA3_dup6692"  "L1PA3_dup7840"  "L1PA3_dup400"   "L1PA3_dup4349" 
## [1013] "L1PA3_dup7550"  "L1PA3_dup1269"  "L1PA2_dup1953"  "L1PA2_dup2155" 
## [1017] "L1PA3_dup4708"  "L1PA2_dup4030"  "L1PA3_dup7864"  "L1PA3_dup5534" 
## [1021] "L1PA2_dup3615"  "L1PA2_dup1805"  "L1PA3_dup1114"  "L1PA3_dup3968" 
## [1025] "L1PA3_dup3880"  "L1PA3_dup165"   "L1PA2_dup71"    "L1PA3_dup2393" 
## [1029] "L1PA3_dup4259"  "L1PA3_dup1279"  "L1PA2_dup3579"  "L1PA2_dup1375" 
## [1033] "L1PA3_dup8420"  "L1PA2_dup727"   "L1PA3_dup358"   "L1PA2_dup4074" 
## [1037] "L1PA3_dup4687"  "L1PA3_dup9095"  "L1PA2_dup142"   "L1HS_dup1182"  
## [1041] "L1PA2_dup1770"  "L1PA2_dup1933"  "L1PA2_dup635"   "L1PA3_dup761"  
## [1045] "L1PA3_dup6434"  "L1PA3_dup4885"  "L1PA3_dup561"   "L1HS_dup800"   
## [1049] "L1PA3_dup8520"  "L1PA3_dup4902"  "L1PA2_dup2289"  "L1PA2_dup2860" 
## [1053] "L1PA2_dup2791"  "L1PA3_dup872"   "L1PA3_dup9280"  "L1PA2_dup200"  
## [1057] "L1PA3_dup124"   "L1PA3_dup6929"  "L1PA3_dup2517"  "L1PA3_dup9998" 
## [1061] "L1PA3_dup5337"  "L1PA3_dup3307"  "L1PA3_dup978"   "L1PA3_dup8007" 
## [1065] "L1HS_dup514"    "L1PA3_dup6385"  "L1PA2_dup663"   "L1HS_dup1536"  
## [1069] "L1HS_dup632"    "L1PA2_dup585"   "L1PA2_dup2680"  "L1PA2_dup1462" 
## [1073] "L1PA2_dup1749"  "L1PA3_dup8571"  "L1PA3_dup5514"  "L1HS_dup788"   
## [1077] "L1HS_dup455"    "L1HS_dup1330"   "L1PA2_dup221"   "L1PA3_dup7951" 
## [1081] "L1PA2_dup1379"  "L1PA3_dup2272"  "L1HS_dup191"    "L1PA3_dup7472" 
## [1085] "L1PA2_dup3736"  "L1HS_dup337"    "L1PA2_dup2988"  "L1PA3_dup4804" 
## [1089] "L1PA3_dup3941"  "L1PA2_dup3742"  "L1PA3_dup1311"  "L1PA3_dup6573" 
## [1093] "L1PA2_dup3437"  "L1PA3_dup6147"  "L1PA3_dup2557"  "L1PA3_dup4492" 
## [1097] "L1PA2_dup1272"  "L1PA3_dup7237"  "L1PA2_dup791"   "L1PA3_dup1010" 
## [1101] "L1PA3_dup10119" "L1PA2_dup922"   "L1PA2_dup1230"  "L1PA3_dup2593" 
## [1105] "L1PA3_dup8663"  "L1PA3_dup10285" "L1PA3_dup4994"  "L1PA2_dup526"  
## [1109] "L1PA3_dup1756"  "L1PA2_dup2245"  "L1PA3_dup373"   "L1PA2_dup927"  
## [1113] "L1PA3_dup2919"  "L1PA3_dup4391"  "L1PA3_dup4888"  "L1PA2_dup4403" 
## [1117] "L1PA2_dup4620"  "L1PA2_dup3771"  "L1PA2_dup1298"  "L1PA3_dup5121" 
## [1121] "L1PA3_dup1710"  "L1PA3_dup4891"  "L1PA3_dup4401"  "L1PA3_dup6002" 
## [1125] "L1PA3_dup7821"  "L1PA2_dup3589"  "L1PA2_dup3805"  "L1PA2_dup410"  
## [1129] "L1PA3_dup7963"  "L1PA2_dup2909"  "L1PA3_dup5680"  "L1PA3_dup10740"
## [1133] "L1PA2_dup1752"  "L1HS_dup1462"   "L1PA3_dup10297" "L1PA2_dup2164" 
## [1137] "L1PA3_dup907"   "L1PA3_dup4122"  "L1PA3_dup7637"  "L1PA2_dup2969" 
## [1141] "L1PA2_dup3531"  "L1PA3_dup3507"  "L1PA3_dup3168"  "L1PA2_dup4440" 
## [1145] "L1PA2_dup4714"  "L1HS_dup138"    "L1PA2_dup530"   "L1PA3_dup7470" 
## [1149] "L1PA2_dup234"   "L1PA3_dup8522"  "L1PA3_dup6550"  "L1PA3_dup2744" 
## [1153] "L1PA3_dup398"   "L1PA2_dup378"   "L1PA3_dup7862"  "L1PA3_dup3757" 
## [1157] "L1PA3_dup3758"  "L1PA3_dup8525"  "L1PA2_dup37"    "L1PA2_dup595"  
## [1161] "L1PA2_dup3136"  "L1HS_dup596"    "L1PA3_dup8872"  "L1HS_dup449"   
## [1165] "L1PA3_dup2721"  "L1PA2_dup4838"  "L1PA2_dup737"   "L1PA2_dup513"  
## [1169] "L1PA2_dup130"   "L1PA3_dup6036"  "L1PA2_dup4905"  "L1PA3_dup6347" 
## [1173] "L1PA2_dup3664"  "L1PA3_dup2413"  "L1PA3_dup2551"  "L1PA3_dup9021" 
## [1177] "L1PA2_dup2091"  "L1PA2_dup1778"  "L1PA3_dup748"   "L1PA2_dup2720" 
## [1181] "L1PA3_dup2760"  "L1PA2_dup662"   "L1PA3_dup529"   "L1PA3_dup527"  
## [1185] "L1PA2_dup1418"  "L1PA3_dup1937"  "L1HS_dup948"    "L1PA3_dup4709" 
## [1189] "L1PA3_dup1800"  "L1PA3_dup9256"  "L1PA2_dup848"   "L1PA3_dup6457" 
## [1193] "L1PA3_dup4277"  "L1HS_dup240"    "L1PA2_dup196"   "L1PA3_dup8903" 
## [1197] "L1PA3_dup1651"  "L1PA3_dup4118"  "L1PA3_dup1"     "L1PA3_dup10686"

Tables of stacked heatmaps

If there is anyone interested, I’ve also saved these matrices to keep the order in which they are shown in figure (return_df = T) to ./ASAP/data/ASAP_PMDBS_snRNAseq/results/tables/.

heatmap_pfc <- asap_heatmap_snRNA(region = c("PFC"), 
                   tes = data_TE_annotation$TE_id, 
                   return_df = T, group_rows = c("type"), gaps_row = length(heatmap_pfc_HERV_order),
                   breaks = seq(0,15,length.out = 52), index_row_reorder = c(heatmap_pfc_HERV_order,heatmap_pfc_L1_order),
                   data = TE_data, group_cols = c("celltype"),
                   order_cols_groups = order_cols_celltype,
                   title = "PFC HERVs + L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
                   exclude_clusters = c(6, 7))

heatmap_put <- asap_heatmap_snRNA(region = c("PUT"), 
                   tes = data_TE_annotation$TE_id, 
                   return_df = T, group_rows = c("type"), gaps_row = length(heatmap_put_HERV_order),
                   breaks = seq(0,15,length.out = 52), index_row_reorder = c(heatmap_put_HERV_order,heatmap_put_L1_order),
                   data = TE_data, group_cols = c("celltype"),
                   order_cols_groups = order_cols_celltype,
                   title = "PUT HERVs + L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
                   exclude_clusters = c(6, 7))

heatmap_amy <- asap_heatmap_snRNA(region = c("AMY"), 
                   tes = data_TE_annotation$TE_id, 
                   return_df = T, group_rows = c("type"), gaps_row = length(heatmap_amy_HERV_order),
                   breaks = seq(0,15,length.out = 52), index_row_reorder = c(heatmap_amy_HERV_order,heatmap_amy_L1_order),
                   data = TE_data, group_cols = c("celltype"),
                   order_cols_groups = order_cols_celltype,
                   title = "AMY HERVs + L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
                   exclude_clusters = c(6, 7))

heatmap_sn <- asap_heatmap_snRNA(region = c("SN"), 
                   tes = data_TE_annotation$TE_id, 
                   return_df = T, group_rows = c("type"), gaps_row = length(heatmap_sn_HERV_order),
                   breaks = seq(0,15,length.out = 52), index_row_reorder = c(heatmap_sn_HERV_order,heatmap_sn_L1_order),
                   data = TE_data, group_cols = c("celltype"),
                   order_cols_groups = order_cols_celltype,
                   title = "SN HERVs + L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
                   exclude_clusters = c(6, 7))

heatmap_sn$norm_counts <- merge(TE_data$te_counts[,c("Geneid", "Chr", "Start", "End", "Strand", "Length")], heatmap_sn$norm_counts, by.y="TE_id", by.x="Geneid")
heatmap_pfc$norm_counts <- merge(TE_data$te_counts[,c("Geneid", "Chr", "Start", "End", "Strand", "Length")], heatmap_pfc$norm_counts, by.y="TE_id", by.x="Geneid")
heatmap_put$norm_counts <- merge(TE_data$te_counts[,c("Geneid", "Chr", "Start", "End", "Strand", "Length")], heatmap_put$norm_counts, by.y="TE_id", by.x="Geneid")
heatmap_amy$norm_counts <- merge(TE_data$te_counts[,c("Geneid", "Chr", "Start", "End", "Strand", "Length")], heatmap_amy$norm_counts, by.y="TE_id", by.x="Geneid")

write.table(heatmap_sn$norm_counts, "/Volumes/MyPassport/ASAP/data/ASAP_PMDBS_snRNAseq/results/tables/heatmap_matrix_SN_FL_HERVs_L1HS_PA3_expressed_bulk_celltype_cluster.tab", sep = ",", quote = F, col.names = T, row.names = F)
write.table(heatmap_pfc$norm_counts, "/Volumes/MyPassport//ASAP/data/ASAP_PMDBS_snRNAseq/results/tables/heatmap_matrix_PFC_FL_HERVs_L1HS_PA3_expressed_bulk_celltype_cluster.tab", sep = ",", quote = F, col.names = T, row.names = F)
write.table(heatmap_put$norm_counts, "/Volumes/MyPassport//ASAP/data/ASAP_PMDBS_snRNAseq/results/tables/heatmap_matrix_PUT_FL_HERVs_L1HS_PA3_expressed_bulk_celltype_cluster.tab", sep = ",", quote = F, col.names = T, row.names = F)
write.table(heatmap_amy$norm_counts, "/Volumes/MyPassport//ASAP/data/ASAP_PMDBS_snRNAseq/results/tables/heatmap_matrix_AMY_FL_HERVs_L1HS_PA3_expressed_bulk_celltype_cluster.tab", sep = ",", quote = F, col.names = T, row.names = F)

Box plots of L1 expression from heatmaps

These matrices also helped to make the boxplots from the same figures (to compare expression between neurons, glia and microglia). We just need to retrieve them per element type (L1/HERVs).

heatmap_pfc_L1 <- asap_heatmap_snRNA(region = c("PFC"), 
                   tes = data_TE_annotation[which(data_TE_annotation$type == "L1"),"TE_id"], 
                   return_df = T, 
                   breaks = seq(0,15,length.out = 52), 
                   data = TE_data, group_cols = c("celltype"),
                   order_cols_groups = order_cols_celltype,
                   title = "PFC L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
                   exclude_clusters = c(6, 7))

heatmap_put_L1 <- asap_heatmap_snRNA(region = c("PUT"), 
                   tes = data_TE_annotation[which(data_TE_annotation$type == "L1"),"TE_id"], 
                   return_df = T, 
                   breaks = seq(0,15,length.out = 52), 
                   data = TE_data, group_cols = c("celltype"),
                   order_cols_groups = order_cols_celltype,
                   title = "PUT L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
                   exclude_clusters = c(6, 7))

heatmap_sn_L1 <- asap_heatmap_snRNA(region = c("SN"), 
                   tes = data_TE_annotation[which(data_TE_annotation$type == "L1"),"TE_id"], 
                   return_df = T, 
                   breaks = seq(0,15,length.out = 52), 
                   data = TE_data, group_cols = c("celltype"),
                   order_cols_groups = order_cols_celltype,
                   title = "SN L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
                   exclude_clusters = c(6, 7))

heatmap_amy_L1 <- asap_heatmap_snRNA(region = c("AMY"), 
                   tes = data_TE_annotation[which(data_TE_annotation$type == "L1"),"TE_id"], 
                   return_df = T, 
                   breaks = seq(0,15,length.out = 52), 
                   data = TE_data, group_cols = c("celltype"),
                   order_cols_groups = order_cols_celltype,
                   title = "AMY L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
                   exclude_clusters = c(6, 7))


merge(data.frame(L1_sum = colMeans(heatmap_pfc_L1$norm_counts[,-ncol(heatmap_pfc_L1$norm_counts)])),
      heatmap_pfc_L1$samplesheet, by="row.names") %>% 
  mutate(celltype_simple = fct_relevel(celltype_simple,c("Neurons","Glia","Microglia"))) %>%
  ggplot(aes(x=celltype_simple, y=L1_sum, color = celltype_simple)) + geom_jitter(height = 0, width = 0.4) + 
  geom_boxplot(width=0.5, alpha = 0.5, outliers = F) + 
  theme_bw() + theme(legend.position = "None") + scale_color_manual(values = c("Neurons" = "#a0dbb0",
                                                                   "Glia" = "#a1a8e6",
                                                                   "Microglia" = "grey")) + 
  labs(y="log2(Pseudobulk normalized\nmean expression)", x="", color="") + stat_compare_means(comparisons = list(c("Neurons", "Microglia"), c("Neurons", "Glia"), c("Microglia", "Glia")), method = "t.test") + ggtitle("PFC >6kbp L1HS-PA3 ")

merge(data.frame(L1_sum = colMeans(heatmap_put_L1$norm_counts[,-ncol(heatmap_put_L1$norm_counts)])),
      heatmap_put_L1$samplesheet, by="row.names") %>% 
  mutate(celltype_simple = fct_relevel(celltype_simple,c("Neurons","Glia","Microglia"))) %>%
  ggplot(aes(x=celltype_simple, y=L1_sum, color = celltype_simple)) + geom_jitter(height = 0, width = 0.4) + 
  geom_boxplot(width=0.5, alpha = 0.5, outliers = F) + 
  theme_bw() + theme(legend.position = "None") + scale_color_manual(values = c("Neurons" = "#a0dbb0",
                                                                   "Glia" = "#a1a8e6",
                                                                   "Microglia" = "grey")) + 
  labs(y="log2(Pseudobulk normalized\nmean expression)", x="", color="") + stat_compare_means(comparisons = list(c("Neurons", "Microglia"), c("Neurons", "Glia"), c("Microglia", "Glia")), method = "t.test") + ggtitle("PUT >6kbp L1HS-PA3 ")

merge(data.frame(L1_sum = colMeans(heatmap_sn_L1$norm_counts[,-ncol(heatmap_sn_L1$norm_counts)])),
      heatmap_sn_L1$samplesheet, by="row.names") %>% 
  mutate(celltype_simple = fct_relevel(celltype_simple,c("Neurons","Glia","Microglia"))) %>%
  ggplot(aes(x=celltype_simple, y=L1_sum, color = celltype_simple)) + geom_jitter(height = 0, width = 0.4) + 
  geom_boxplot(width=0.5, alpha = 0.5, outliers = F) + 
  theme_bw() + theme(legend.position = "None") + scale_color_manual(values = c("Neurons" = "#a0dbb0",
                                                                   "Glia" = "#a1a8e6",
                                                                   "Microglia" = "grey")) + 
  labs(y="log2(Pseudobulk normalized\nmean expression)", x="", color="") + stat_compare_means(comparisons = list(c("Neurons", "Microglia"), c("Neurons", "Glia"), c("Microglia", "Glia")), method = "t.test") + ggtitle("SN >6kbp L1HS-PA3 ")

merge(data.frame(L1_sum = colMeans(heatmap_amy_L1$norm_counts[,-ncol(heatmap_amy_L1$norm_counts)])),
      heatmap_amy_L1$samplesheet, by="row.names") %>% 
  mutate(celltype_simple = fct_relevel(celltype_simple,c("Neurons","Glia","Microglia"))) %>%
  ggplot(aes(x=celltype_simple, y=L1_sum, color = celltype_simple)) + geom_jitter(height = 0, width = 0.4) + 
  geom_boxplot(width=0.5, alpha = 0.5, outliers = F) + 
  theme_bw() + theme(legend.position = "None") + scale_color_manual(values = c("Neurons" = "#a0dbb0",
                                                                   "Glia" = "#a1a8e6",
                                                                   "Microglia" = "grey")) + 
  labs(y="log2(Pseudobulk normalized\nmean expression)", x="", color="") + stat_compare_means(comparisons = list(c("Neurons", "Microglia"), c("Neurons", "Glia"), c("Microglia", "Glia")), method = "t.test") + ggtitle("AMY >6kbp L1HS-PA3 ")

Box plots of HERV expression from heatmaps

Same method for HERVs!

heatmap_amy_HERV <- asap_heatmap_snRNA(region = c("AMY"), 
                   tes = data_TE_annotation[which(data_TE_annotation$type == "HERV"),"TE_id"], 
                   return_df = T, 
                   breaks = seq(0,15,length.out = 60), 
                   data = TE_data, group_cols = c("celltype"),
                   order_cols_groups = order_cols_celltype,
                   title = "AMY HERVs: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
                   exclude_clusters = c(6, 7))

heatmap_pfc_HERV <- asap_heatmap_snRNA(region = c("PFC"), 
                   tes = data_TE_annotation[which(data_TE_annotation$type == "HERV"),"TE_id"], 
                   return_df = T, 
                   breaks = seq(0,15,length.out = 60), 
                   data = TE_data, group_cols = c("celltype"),
                   order_cols_groups = order_cols_celltype,
                   title = "PFC HERVs: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
                   exclude_clusters = c(6, 7))

heatmap_put_HERV <- asap_heatmap_snRNA(region = c("PUT"), 
                   tes = data_TE_annotation[which(data_TE_annotation$type == "HERV"),"TE_id"], 
                   return_df = T, 
                   breaks = seq(0,15,length.out = 60), 
                   data = TE_data, group_cols = c("celltype"),
                   order_cols_groups = order_cols_celltype,
                   title = "PUT HERVs: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
                   exclude_clusters = c(6, 7))

heatmap_sn_HERV <- asap_heatmap_snRNA(region = c("SN"), 
                   tes = data_TE_annotation[which(data_TE_annotation$type == "HERV"),"TE_id"], 
                   return_df = T, 
                   breaks = seq(0,15,length.out = 60), 
                   data = TE_data, group_cols = c("celltype"),
                   order_cols_groups = order_cols_celltype,
                   title = "SN HERVs: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation,
                   exclude_clusters = c(6, 7))


merge(data.frame(HERV_sum = colMeans(heatmap_pfc_HERV$norm_counts[,-ncol(heatmap_pfc_HERV$norm_counts)])),
      heatmap_pfc_HERV$samplesheet, by="row.names") %>% 
  mutate(celltype_simple = fct_relevel(celltype_simple,c("Neurons","Glia","Microglia"))) %>%
  ggplot(aes(x=celltype_simple, y=HERV_sum, color = celltype_simple)) + geom_jitter(height = 0, width = 0.4) + 
  geom_boxplot(width=0.5, alpha = 0.5, outliers = F) + 
  theme_bw() + theme(legend.position = "None") + scale_color_manual(values = c("Neurons" = "#a0dbb0",
                                                                   "Glia" = "#a1a8e6",
                                                                   "Microglia" = "grey")) + 
  labs(y="log2(Pseudobulk normalized\nmean expression)", x="", color="") + stat_compare_means(comparisons = list(c("Neurons", "Microglia"), c("Neurons", "Glia"), c("Microglia", "Glia")), method = "t.test") + ggtitle("PFC HERVs ")

merge(data.frame(HERV_sum = colMeans(heatmap_put_HERV$norm_counts[,-ncol(heatmap_put_HERV$norm_counts)])),
      heatmap_put_HERV$samplesheet, by="row.names") %>% 
  mutate(celltype_simple = fct_relevel(celltype_simple,c("Neurons","Glia","Microglia"))) %>%
  ggplot(aes(x=celltype_simple, y=HERV_sum, color = celltype_simple)) + geom_jitter(height = 0, width = 0.4) + 
  geom_boxplot(width=0.5, alpha = 0.5, outliers = F) + 
  theme_bw() + theme(legend.position = "None") + scale_color_manual(values = c("Neurons" = "#a0dbb0",
                                                                   "Glia" = "#a1a8e6",
                                                                   "Microglia" = "grey")) + 
  labs(y="log2(Pseudobulk normalized\nmean expression)", x="", color="") + stat_compare_means(comparisons = list(c("Neurons", "Microglia"), c("Neurons", "Glia"), c("Microglia", "Glia")), method = "t.test") + ggtitle("PUT HERVs ")

merge(data.frame(HERV_sum = colMeans(heatmap_sn_HERV$norm_counts[,-ncol(heatmap_sn_HERV$norm_counts)])),
      heatmap_sn_HERV$samplesheet, by="row.names") %>% 
  mutate(celltype_simple = fct_relevel(celltype_simple,c("Neurons","Glia","Microglia"))) %>%
  ggplot(aes(x=celltype_simple, y=HERV_sum, color = celltype_simple)) + geom_jitter(height = 0, width = 0.4) + 
  geom_boxplot(width=0.5, alpha = 0.5, outliers = F) + 
  theme_bw() + theme(legend.position = "None") + scale_color_manual(values = c("Neurons" = "#a0dbb0",
                                                                   "Glia" = "#a1a8e6",
                                                                   "Microglia" = "grey")) + 
  labs(y="log2(Pseudobulk normalized\nmean expression)", x="", color="") + stat_compare_means(comparisons = list(c("Neurons", "Microglia"), c("Neurons", "Glia"), c("Microglia", "Glia")), method = "t.test") + ggtitle("SN HERVs ")

merge(data.frame(HERV_sum = colMeans(heatmap_amy_HERV$norm_counts[,-ncol(heatmap_amy_HERV$norm_counts)])),
      heatmap_amy_HERV$samplesheet, by="row.names") %>% 
  mutate(celltype_simple = fct_relevel(celltype_simple,c("Neurons","Glia","Microglia"))) %>%
  ggplot(aes(x=celltype_simple, y=HERV_sum, color = celltype_simple)) + geom_jitter(height = 0, width = 0.4) + 
  geom_boxplot(width=0.5, alpha = 0.5, outliers = F) + 
  theme_bw() + theme(legend.position = "None") + scale_color_manual(values = c("Neurons" = "#a0dbb0",
                                                                   "Glia" = "#a1a8e6",
                                                                   "Microglia" = "grey")) + 
  labs(y="log2(Pseudobulk normalized\nmean expression)", x="", color="") + stat_compare_means(comparisons = list(c("Neurons", "Microglia"), c("Neurons", "Glia"), c("Microglia", "Glia")), method = "t.test") + ggtitle("AMY HERVs ")

---

9. Negative controls

Important to validate that our method is not picking up noise. Here we plot elements which were not found to be expressed in our deep bulk RNAseq data.

• Heatmap visualization of >6kbp L1HS-L1PA3 and HERVs which were NOT found to be expressed in bulk RNAseq.
• Excluded clusters 6 (VLMC) and 7 (Tcells) due to low number of nuclei.

# L1s
L1s_notexpressed <- read.table("/Volumes/MyPassport/ASAP/code/ASAP_PMDBS_bulkRNAseq/results/tables/not_expressed_FL_L1HS_L1PA3.tab")$V1
# HERVs
HERVs_notexpressed <- read.table("/Volumes/MyPassport/ASAP/code/ASAP_PMDBS_bulkRNAseq/results/tables/not_expressed_fl_hervs.tab")$V1

data_TE_annotation <- data.frame("TE_id" = c(L1s_notexpressed, HERVs_notexpressed),
                                 "type" = ifelse(startsWith(c(L1s_notexpressed, HERVs_notexpressed), "HERV"), "HERV", "L1"))
rownames(data_TE_annotation) <- data_TE_annotation$TE_id

asap_heatmap_snRNA(region = c("PFC", "PUT", "AMY", "SN"), 
                   tes = HERVs_notexpressed, 
                   return_df = F, 
                   breaks = seq(0,15,length.out = 52), 
                   data = TE_data, 
                   group_cols = c("celltype"), 
                   order_cols_groups = order_cols_celltype,
                   title = "Not expressed HERVs: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation)

## $heatmap
## 
## $order_cols
##   [1] "AA84_ASAP71_PD_NP19-16_PUT_0"     "AA79_ASAP64_PD_NP16-162_PUT_0"   
##   [3] "AA_ASAP141_ctrl_NP19-218_PUT_0"   "DA805_ASAP56_ctrl_NP19-37_AMY_0" 
##   [5] "DA474_ASAP24_PD_NP16-25_AMY_0"    "DA428_ASAP13_ctrl_NP16-161_PFC_0"
##   [7] "AA_ASAP86_NP18-148_ctrl_PFC_0"    "AA_ASAP85_NP18-46_ctrl_PFC_0"    
##   [9] "DA476_ASAP10_PD_NP16-25_PFC_0"    "AA_ASAP90_ctrl_NP16-293_PFC_0"   
##  [11] "AA_ASAP89_ctrl_NP16-284_PFC_0"    "AA_ASAP116_PD_NP22-55_PFC_0"     
##  [13] "AA_ASAP91_ctrl_NP17-20_PFC_0"     "AA_ASAP81_PD_NP21-208_PFC_0"     
##  [15] "MJ_ASAP14_ctrl_NP16-164_PFC_0"    "AA_ASAP151_PD_NP17-232_PFC_0"    
##  [17] "AA_ASAP83_NP16-119_ctrl_PFC_0"    "DA430_ASAP9_PD_NP16-162_PFC_0"   
##  [19] "DA499_ASAP44_PD_NP19-255_PFC_0"   "DA509_ASAP36_PD_NP19-16_PFC_0"   
##  [21] "DA480_ASAP15_ctrl_NP16-21_PFC_0"  "AA_ASAP110_ctrl_NP16-119_AMY_0"  
##  [23] "ASAP155_ctrl_NP23-21_PFC_0"       "DA795_ASAP55_ctrl_NP19-37_PFC_0" 
##  [25] "AA_ASAP153_ctrl_NP19-137_PFC_0"   "DA490_ASAP11_PD_P73_PFC_0"       
##  [27] "AA_ASAP138_PD_NP16-285_PUT_0"     "AA_ASAP114_PD_NP21-57_AMY_0"     
##  [29] "AA_ASAP98_ctrl_NP16-119_PUT_0"    "DA778_ASAP31_PD_NP18-117_AMY_0"  
##  [31] "AA82_ASAP68_PD_NP18-117_PUT_0"    "AA_ASAP100_ctrl_NP18-148_PUT_0"  
##  [33] "AA_ASAP152_PD_NP19-91_PFC_0"      "AA_ASAP97_PD_NP21-57_PUT_0"      
##  [35] "AA87_ASAP76_ctrl_NP18-159_PUT_0"  "DA780_ASAP37_PD_NP19-16_AMY_0"   
##  [37] "DA793_ASAP53_ctrl_NP19-36_AMY_0"  "DA811_ASAP18_PD_NP16-140_AMY_0"  
##  [39] "DA802_ASAP40_PD_NP19-23_AMY_0"    "AA71_ASAP70_PD_NP18-304_PUT_0"   
##  [41] "AA74_ASAP62_PD_NP16-140_PUT_0"    "DA783_ASAP45_PD_NP19-255_AMY_0"  
##  [43] "AA_ASAP115_PD_NP21-208_AMY_0"     "DA806_ASAP58_ctrl_NP19-45_PFC_0" 
##  [45] "DA488_ASAP16_ctrl_PT231_PFC_0"    "DA810_ASAP34_PD_NP18-304_PFC_0"  
##  [47] "DA432_ASAP12_PD_P74_PFC_0"        "AA_ASAP80_PD_NP21-57_PFC_0"      
##  [49] "AA_ASAP145_ctrl_NP19-218_PFC_0"   "DA813_ASAP17_PD_NP16-140_PFC_0"  
##  [51] "DA775_ASAP22_PD_NP16-269_PFC_0"   "DA791_ASAP50_ctrl_NP18-159_AMY_0"
##  [53] "DA777_ASAP28_PD_NP17-191_PFC_0"   "AA_ASAP82_PD_NP21-217_PFC_0"     
##  [55] "DA809_ASAP30_PD_NP18-117_PFC_0"   "DA804_ASAP49_ctrl_NP18-159_PFC_0"
##  [57] "DA775_ASAP22_PD_NP16-269_PFC_1"   "AA_ASAP123_ctrl_NP19-218_AMY_1"  
##  [59] "DA806_ASAP58_ctrl_NP19-45_PFC_1"  "AA79_ASAP64_PD_NP16-162_PUT_1"   
##  [61] "AA_ASAP115_PD_NP21-208_AMY_1"     "DA805_ASAP56_ctrl_NP19-37_AMY_1" 
##  [63] "DA811_ASAP18_PD_NP16-140_AMY_1"   "DA480_ASAP15_ctrl_NP16-21_PFC_1" 
##  [65] "AA71_ASAP70_PD_NP18-304_PUT_1"    "AA74_ASAP62_PD_NP16-140_PUT_1"   
##  [67] "AA_ASAP137_PD_NP23-21_SN_1"       "DA793_ASAP53_ctrl_NP19-36_AMY_1" 
##  [69] "AA_ASAP119_PD_NP22-55_AMY_1"      "AA_ASAP151_PD_NP17-232_PFC_1"    
##  [71] "AA_ASAP100_ctrl_NP18-148_PUT_1"   "DA490_ASAP11_PD_P73_PFC_1"       
##  [73] "AA_ASAP81_PD_NP21-208_PFC_1"      "DA809_ASAP30_PD_NP18-117_PFC_1"  
##  [75] "AA_ASAP86_NP18-148_ctrl_PFC_1"    "DA778_ASAP31_PD_NP18-117_AMY_1"  
##  [77] "AA_ASAP153_ctrl_NP19-137_PFC_1"   "AA_ASAP124_ctrl_NP22-37_AMY_1"   
##  [79] "AA_ASAP89_ctrl_NP16-284_PFC_1"    "DA474_ASAP24_PD_NP16-25_AMY_1"   
##  [81] "AA_ASAP91_ctrl_NP17-20_PFC_1"     "AA_ASAP131_PD_NP23-21_AMY_1"     
##  [83] "AA_ASAP128_PD_NP21-04_AMY_1"      "AA_ASAP109_PD_NP21-217_AMY_1"    
##  [85] "AA_ASAP118_PD_NP22-55_SN_1"       "AA_ASAP144_PD_NP19-137_PUT_1"    
##  [87] "AA_ASAP85_NP18-46_ctrl_PFC_1"     "AA_ASAP129_ctrl_NP22-37_SN_1"    
##  [89] "AA_ASAP90_ctrl_NP16-293_PFC_1"    "DA777_ASAP28_PD_NP17-191_PFC_1"  
##  [91] "AA_ASAP126_PD_NP19-137_AMY_1"     "AA_ASAP92_ctrl_NP16-284_PUT_1"   
##  [93] "ASAP155_ctrl_NP23-21_PFC_1"       "AA_ASAP82_PD_NP21-217_PFC_1"     
##  [95] "DA795_ASAP55_ctrl_NP19-37_PFC_1"  "AA_ASAP121_PD_NP17-232_AMY_1"    
##  [97] "DA487_ASAP8_ctrl_PT231_SN_1"      "AA_ASAP152_PD_NP19-91_PFC_1"     
##  [99] "AA_ASAP110_ctrl_NP16-119_AMY_1"   "AA_ASAP114_PD_NP21-57_AMY_1"     
## [101] "AA_ASAP116_PD_NP22-55_PFC_1"      "DA509_ASAP36_PD_NP19-16_PFC_1"   
## [103] "DA512_ASAP60_ctrl_NP19-45_AMY_1"  "AA_ASAP139_PD_NP17-232_PUT_1"    
## [105] "AA_ASAP145_ctrl_NP19-218_PFC_1"   "AA84_ASAP71_PD_NP19-16_PUT_1"    
## [107] "AA_ASAP80_PD_NP21-57_PFC_1"       "AA_ASAP117_PD_NP22-55_PUT_1"     
## [109] "DA792_ASAP51_ctrl_NP19-36_SN_1"   "AA_ASAP87_PD_NP21-208_PUT_1"     
## [111] "DA488_ASAP16_ctrl_PT231_PFC_1"    "DA430_ASAP9_PD_NP16-162_PFC_1"   
## [113] "DA810_ASAP34_PD_NP18-304_PFC_1"   "DA432_ASAP12_PD_P74_PFC_1"       
## [115] "DA476_ASAP10_PD_NP16-25_PFC_1"    "AA87_ASAP76_ctrl_NP18-159_PUT_1" 
## [117] "AA_ASAP83_NP16-119_ctrl_PFC_1"    "DA428_ASAP13_ctrl_NP16-161_PFC_1"
## [119] "DA499_ASAP44_PD_NP19-255_PFC_1"   "DA783_ASAP45_PD_NP19-255_AMY_1"  
## [121] "MJ_ASAP14_ctrl_NP16-164_PFC_1"    "AA_ASAP88_PD_NP21-217_PUT_1"     
## [123] "DA780_ASAP37_PD_NP19-16_AMY_1"    "DA791_ASAP50_ctrl_NP18-159_AMY_1"
## [125] "AA_ASAP113_ctrl_NP18-148_AMY_1"   "DA801_ASAP53_ctrl_NP19-36_AMY_1" 
## [127] "DA804_ASAP49_ctrl_NP18-159_PFC_1" "DA802_ASAP40_PD_NP19-23_AMY_1"   
## [129] "DA802_ASAP40_PD_NP19-23_AMY_2"    "AA_ASAP152_PD_NP19-91_PFC_2"     
## [131] "AA_ASAP128_PD_NP21-04_AMY_2"      "AA_ASAP145_ctrl_NP19-218_PFC_2"  
## [133] "AA_ASAP102_PD_NP21-208_SN_2"      "AA_ASAP99_ctrl_NP16-284_SN_2"    
## [135] "DA796_ASAP57_ctrl_NP19-45_SN_2"   "AA87_ASAP76_ctrl_NP18-159_PUT_2" 
## [137] "DA809_ASAP30_PD_NP18-117_PFC_2"   "AA_ASAP151_PD_NP17-232_PFC_2"    
## [139] "AA_ASAP129_ctrl_NP22-37_SN_2"     "DA814_ASAP35_PD_NP18-304_AMY_2"  
## [141] "AA_ASAP140_PD_NP19-91_PUT_2"      "AA_ASAP101_PD_NP21-57_SN_2"      
## [143] "AA_ASAP100_ctrl_NP18-148_PUT_2"   "AA_ASAP112_ctrl_NP16-293_AMY_2"  
## [145] "DA811_ASAP18_PD_NP16-140_AMY_2"   "ASAP122_PD_NP19-91_AMY_2"        
## [147] "DA473_ASAP38_PD_NP19-23_SN_2"     "AA_ASAP119_PD_NP22-55_AMY_2"     
## [149] "AA_ASAP118_PD_NP22-55_SN_2"       "MJ_ASAP14_ctrl_NP16-164_PFC_2"   
## [151] "AA_ASAP93_ctrl_NP16-293_PUT_2"    "AA_ASAP134_PD_NP19-91_SN_2"      
## [153] "AA_ASAP86_NP18-148_ctrl_PFC_2"    "AA_ASAP117_PD_NP22-55_PUT_2"     
## [155] "DA487_ASAP8_ctrl_PT231_SN_2"      "AA_ASAP113_ctrl_NP18-148_AMY_2"  
## [157] "DA499_ASAP44_PD_NP19-255_PFC_2"   "AA_ASAP108_ctrl_NP18-148_SN_2"   
## [159] "AA_ASAP139_PD_NP17-232_PUT_2"     "AA82_ASAP68_PD_NP18-117_PUT_2"   
## [161] "AA_ASAP96_ctrl_NP18-46_PUT_2"     "DA782_ASAP41_PD_NP19-108_SN_2"   
## [163] "DA479_ASAP7_ctrl_NP16-21_SN_2"    "AA88_ASAP77_ctrl_NP19-36_PUT_2"  
## [165] "AA_ASAP104_ctrl_NP16-119_SN_2"    "AA_ASAP150_PD_NP16-285_PFC_2"    
## [167] "AA_ASAP126_PD_NP19-137_AMY_2"     "DA784_ASAP46_ctrl_NP17-256_SN_2" 
## [169] "AA_ASAP154_ctrl_NP21-04_PFC_2"    "AA_ASAP94_ctrl_NP17-20_PUT_2"    
## [171] "AA_ASAP120_PD_NP16-285_AMY_2"     "AA_ASAP105_ctrl_NP16-293_SN_2"   
## [173] "AA_ASAP81_PD_NP21-208_PFC_2"      "AA_ASAP153_ctrl_NP19-137_PFC_2"  
## [175] "AA_ASAP91_ctrl_NP17-20_PFC_2"     "DA490_ASAP11_PD_P73_PFC_2"       
## [177] "DA785_ASAP47_ctrl_NP17-256_PFC_2" "DA783_ASAP45_PD_NP19-255_AMY_2"  
## [179] "DA433_ASAP5_ctrl_NP16-161_SN_2"   "DA431_ASAP4_PD_P74_SN_2"         
## [181] "AA86_ASAP73_PD_NP19-108_PUT_2"    "AA_ASAP84_NP17-216_ctrl_PFC_2"   
## [183] "AA_ASAP109_PD_NP21-217_AMY_2"     "AA85_ASAP72_PD_NP19-23_PUT_2"    
## [185] "AA_ASAP82_PD_NP21-217_PFC_2"      "AA_ASAP90_ctrl_NP16-293_PFC_2"   
## [187] "DA509_ASAP36_PD_NP19-16_PFC_2"    "AA_ASAP103_PD_NP21-217_SN_2"     
## [189] "AA76_ASAP74_PD_NP19-255_PUT_2"    "AA_ASAP88_PD_NP21-217_PUT_2"     
## [191] "DA475_ASAP2_PD_NP16-25_SN_2"      "AA_ASAP131_PD_NP23-21_AMY_2"     
## [193] "AA_ASAP92_ctrl_NP16-284_PUT_2"    "DA489_ASAP3_PD_P73_SN_2"         
## [195] "DA429_ASAP1_PD_NP16-162_SN_2"     "DA791_ASAP50_ctrl_NP18-159_AMY_2"
## [197] "AA89_ASAP78_ctrl_NP19-37_PUT_2"   "AA_ASAP124_ctrl_NP22-37_AMY_2"   
## [199] "AA_ASAP133_PD_NP17-232_SN_2"      "AA_ASAP121_PD_NP17-232_AMY_2"    
## [201] "AA_ASAP132_PD_NP16-285_SN_2"      "AA_ASAP123_ctrl_NP19-218_AMY_2"  
## [203] "AA_ASAP144_PD_NP19-137_PUT_2"     "AA77_ASAP61_PD_NP16-25_PUT_2"    
## [205] "AA_ASAP89_ctrl_NP16-284_PFC_2"    "DA794_ASAP54_ctrl_NP19-37_SN_2"  
## [207] "DA430_ASAP9_PD_NP16-162_PFC_2"    "DA428_ASAP13_ctrl_NP16-161_PFC_2"
## [209] "DA806_ASAP58_ctrl_NP19-45_PFC_2"  "DA474_ASAP24_PD_NP16-25_AMY_2"   
## [211] "AA_ASAP141_ctrl_NP19-218_PUT_2"   "DA476_ASAP10_PD_NP16-25_PFC_2"   
## [213] "AA_ASAP83_NP16-119_ctrl_PFC_2"    "DA792_ASAP51_ctrl_NP19-36_SN_2"  
## [215] "DA793_ASAP53_ctrl_NP19-36_AMY_2"  "ASAP155_ctrl_NP23-21_PFC_2"      
## [217] "DA775_ASAP22_PD_NP16-269_PFC_2"   "AA_ASAP110_ctrl_NP16-119_AMY_2"  
## [219] "AA71_ASAP70_PD_NP18-304_PUT_2"    "DA810_ASAP34_PD_NP18-304_PFC_2"  
## [221] "AA79_ASAP64_PD_NP16-162_PUT_2"    "AA74_ASAP62_PD_NP16-140_PUT_2"   
## [223] "DA511_ASAP21_PD_NP16-269_SN_2"    "AA_ASAP138_PD_NP16-285_PUT_2"    
## [225] "MJ_ASAP6_ctrl_NP16-164_SN_2"      "AA_ASAP98_ctrl_NP16-119_PUT_2"   
## [227] "DA480_ASAP15_ctrl_NP16-21_PFC_2"  "DA488_ASAP16_ctrl_PT231_PFC_2"   
## [229] "AA_ASAP115_PD_NP21-208_AMY_2"     "DA432_ASAP12_PD_P74_PFC_2"       
## [231] "AA_ASAP137_PD_NP23-21_SN_2"       "DA807_ASAP29_PD_NP17-191_AMY_2"  
## [233] "AA_ASAP127_ctrl_NP19-218_SN_2"    "AA73_ASAP65_PD_NP16-269_PUT_2"   
## [235] "AA_ASAP87_PD_NP21-208_PUT_2"      "DA512_ASAP60_ctrl_NP19-45_AMY_2" 
## [237] "AA_ASAP135_PD_NP19-137_SN_2"      "DA780_ASAP37_PD_NP19-16_AMY_2"   
## [239] "DA801_ASAP53_ctrl_NP19-36_AMY_2"  "AA84_ASAP71_PD_NP19-16_PUT_2"    
## [241] "AA81_ASAP67_PD_NP17-191_PUT_2"    "AA83_ASAP69_PD_NP18-287_PUT_2"   
## [243] "AA_ASAP116_PD_NP22-55_PFC_2"      "AA_ASAP80_PD_NP21-57_PFC_2"      
## [245] "AA_ASAP114_PD_NP21-57_AMY_2"      "DA808_ASAP41_PD_NP19-108_PFC_2"  
## [247] "AA_ASAP97_PD_NP21-57_PUT_2"       "DA778_ASAP31_PD_NP18-117_AMY_2"  
## [249] "DA804_ASAP49_ctrl_NP18-159_PFC_2" "AA_ASAP146_PD_NP21-04_PUT_2"     
## [251] "DA795_ASAP55_ctrl_NP19-37_PFC_2"  "DA805_ASAP56_ctrl_NP19-37_AMY_2" 
## [253] "AA_ASAP120_PD_NP16-285_AMY_3"     "AA_ASAP112_ctrl_NP16-293_AMY_3"  
## [255] "ASAP122_PD_NP19-91_AMY_3"         "AA_ASAP115_PD_NP21-208_AMY_3"    
## [257] "AA_ASAP109_PD_NP21-217_AMY_3"     "AA_ASAP84_NP17-216_ctrl_PFC_3"   
## [259] "AA_ASAP86_NP18-148_ctrl_PFC_3"    "DA785_ASAP47_ctrl_NP17-256_PFC_3"
## [261] "AA_ASAP91_ctrl_NP17-20_PFC_3"     "DA777_ASAP28_PD_NP17-191_PFC_3"  
## [263] "AA_ASAP116_PD_NP22-55_PFC_3"      "DA432_ASAP12_PD_P74_PFC_3"       
## [265] "AA89_ASAP78_ctrl_NP19-37_PUT_3"   "AA_ASAP93_ctrl_NP16-293_PUT_3"   
## [267] "AA86_ASAP73_PD_NP19-108_PUT_3"    "AA_ASAP97_PD_NP21-57_PUT_3"      
## [269] "AA_ASAP88_PD_NP21-217_PUT_3"      "DA796_ASAP57_ctrl_NP19-45_SN_3"  
## [271] "AA_ASAP133_PD_NP17-232_SN_3"      "AA_ASAP136_PD_NP21-04_SN_3"      
## [273] "AA_ASAP131_PD_NP23-21_AMY_3"      "AA_ASAP104_ctrl_NP16-119_SN_3"   
## [275] "DA499_ASAP44_PD_NP19-255_PFC_3"   "AA_ASAP119_PD_NP22-55_AMY_3"     
## [277] "AA_ASAP134_PD_NP19-91_SN_3"       "AA_ASAP90_ctrl_NP16-293_PFC_3"   
## [279] "AA73_ASAP65_PD_NP16-269_PUT_3"    "AA88_ASAP77_ctrl_NP19-36_PUT_3"  
## [281] "AA_ASAP145_ctrl_NP19-218_PFC_3"   "AA_ASAP99_ctrl_NP16-284_SN_3"    
## [283] "DA490_ASAP11_PD_P73_PFC_3"        "AA74_ASAP62_PD_NP16-140_PUT_3"   
## [285] "DA784_ASAP46_ctrl_NP17-256_SN_3"  "MJ_ASAP14_ctrl_NP16-164_PFC_3"   
## [287] "AA_ASAP129_ctrl_NP22-37_SN_3"     "DA782_ASAP41_PD_NP19-108_SN_3"   
## [289] "DA778_ASAP31_PD_NP18-117_AMY_3"   "DA803_ASAP48_ctrl_NP17-256_AMY_3"
## [291] "AA_ASAP92_ctrl_NP16-284_PUT_3"    "AA_ASAP96_ctrl_NP18-46_PUT_3"    
## [293] "ASAP155_ctrl_NP23-21_PFC_3"       "AA_ASAP152_PD_NP19-91_PFC_3"     
## [295] "DA783_ASAP45_PD_NP19-255_AMY_3"   "AA_ASAP103_PD_NP21-217_SN_3"     
## [297] "AA_ASAP101_PD_NP21-57_SN_3"       "AA_ASAP124_ctrl_NP22-37_AMY_3"   
## [299] "DA811_ASAP18_PD_NP16-140_AMY_3"   "DA475_ASAP2_PD_NP16-25_SN_3"     
## [301] "AA_ASAP111_ctrl_NP16-284_AMY_3"   "AA_ASAP98_ctrl_NP16-119_PUT_3"   
## [303] "DA473_ASAP38_PD_NP19-23_SN_3"     "AA76_ASAP74_PD_NP19-255_PUT_3"   
## [305] "DA431_ASAP4_PD_P74_SN_3"          "AA_ASAP149_PD_NP23-21_PUT_3"     
## [307] "AA_ASAP146_PD_NP21-04_PUT_3"      "AA_ASAP80_PD_NP21-57_PFC_3"      
## [309] "AA87_ASAP76_ctrl_NP18-159_PUT_3"  "DA489_ASAP3_PD_P73_SN_3"         
## [311] "AA_ASAP87_PD_NP21-208_PUT_3"      "AA_ASAP100_ctrl_NP18-148_PUT_3"  
## [313] "AA_ASAP82_PD_NP21-217_PFC_3"      "DA795_ASAP55_ctrl_NP19-37_PFC_3" 
## [315] "AA_ASAP154_ctrl_NP21-04_PFC_3"    "DA480_ASAP15_ctrl_NP16-21_PFC_3" 
## [317] "AA_ASAP94_ctrl_NP17-20_PUT_3"     "MJ_ASAP6_ctrl_NP16-164_SN_3"     
## [319] "AA_ASAP139_PD_NP17-232_PUT_3"     "DA479_ASAP7_ctrl_NP16-21_SN_3"   
## [321] "AA82_ASAP68_PD_NP18-117_PUT_3"    "DA487_ASAP8_ctrl_PT231_SN_3"     
## [323] "AA_ASAP132_PD_NP16-285_SN_3"      "DA809_ASAP30_PD_NP18-117_PFC_3"  
## [325] "DA791_ASAP50_ctrl_NP18-159_AMY_3" "AA_ASAP113_ctrl_NP18-148_AMY_3"  
## [327] "DA802_ASAP40_PD_NP19-23_AMY_3"    "AA_ASAP108_ctrl_NP18-148_SN_3"   
## [329] "DA512_ASAP60_ctrl_NP19-45_AMY_3"  "AA85_ASAP72_PD_NP19-23_PUT_3"    
## [331] "AA_ASAP118_PD_NP22-55_SN_3"       "AA_ASAP150_PD_NP16-285_PFC_3"    
## [333] "DA430_ASAP9_PD_NP16-162_PFC_3"    "AA77_ASAP61_PD_NP16-25_PUT_3"    
## [335] "AA_ASAP151_PD_NP17-232_PFC_3"     "AA_ASAP138_PD_NP16-285_PUT_3"    
## [337] "AA_ASAP121_PD_NP17-232_AMY_3"     "AA_ASAP142_ctrl_NP22-37_PUT_3"   
## [339] "AA_ASAP117_PD_NP22-55_PUT_3"      "DA775_ASAP22_PD_NP16-269_PFC_3"  
## [341] "AA_ASAP105_ctrl_NP16-293_SN_3"    "AA_ASAP89_ctrl_NP16-284_PFC_3"   
## [343] "AA_ASAP140_PD_NP19-91_PUT_3"      "AA_ASAP128_PD_NP21-04_AMY_3"     
## [345] "DA804_ASAP49_ctrl_NP18-159_PFC_3" "DA780_ASAP37_PD_NP19-16_AMY_3"   
## [347] "DA807_ASAP29_PD_NP17-191_AMY_3"   "DA792_ASAP51_ctrl_NP19-36_SN_3"  
## [349] "DA428_ASAP13_ctrl_NP16-161_PFC_3" "AA84_ASAP71_PD_NP19-16_PUT_3"    
## [351] "AA_ASAP83_NP16-119_ctrl_PFC_3"    "AA79_ASAP64_PD_NP16-162_PUT_3"   
## [353] "DA429_ASAP1_PD_NP16-162_SN_3"     "AA83_ASAP69_PD_NP18-287_PUT_3"   
## [355] "DA509_ASAP36_PD_NP19-16_PFC_3"    "AA_ASAP127_ctrl_NP19-218_SN_3"   
## [357] "DA488_ASAP16_ctrl_PT231_PFC_3"    "DA433_ASAP5_ctrl_NP16-161_SN_3"  
## [359] "AA_ASAP102_PD_NP21-208_SN_3"      "AA_ASAP137_PD_NP23-21_SN_3"      
## [361] "AA_ASAP141_ctrl_NP19-218_PUT_3"   "AA81_ASAP67_PD_NP17-191_PUT_3"   
## [363] "DA476_ASAP10_PD_NP16-25_PFC_3"    "AA_ASAP144_PD_NP19-137_PUT_3"    
## [365] "DA793_ASAP53_ctrl_NP19-36_AMY_3"  "AA_ASAP110_ctrl_NP16-119_AMY_3"  
## [367] "DA474_ASAP24_PD_NP16-25_AMY_3"    "AA_ASAP135_PD_NP19-137_SN_3"     
## [369] "DA511_ASAP21_PD_NP16-269_SN_3"    "DA806_ASAP58_ctrl_NP19-45_PFC_3" 
## [371] "DA794_ASAP54_ctrl_NP19-37_SN_3"   "AA_ASAP123_ctrl_NP19-218_AMY_3"  
## [373] "DA805_ASAP56_ctrl_NP19-37_AMY_3"  "DA810_ASAP34_PD_NP18-304_PFC_3"  
## [375] "AA71_ASAP70_PD_NP18-304_PUT_3"    "DA801_ASAP53_ctrl_NP19-36_AMY_3" 
## [377] "AA_ASAP114_PD_NP21-57_AMY_3"      "AA_ASAP101_PD_NP21-57_SN_5"      
## [379] "AA_ASAP97_PD_NP21-57_PUT_5"       "AA_ASAP80_PD_NP21-57_PFC_5"      
## [381] "AA87_ASAP76_ctrl_NP18-159_PUT_5"  "AA_ASAP85_NP18-46_ctrl_PFC_5"    
## [383] "AA_ASAP152_PD_NP19-91_PFC_5"      "DA489_ASAP3_PD_P73_SN_5"         
## [385] "AA_ASAP103_PD_NP21-217_SN_5"      "DA783_ASAP45_PD_NP19-255_AMY_5"  
## [387] "DA803_ASAP48_ctrl_NP17-256_AMY_5" "AA_ASAP89_ctrl_NP16-284_PFC_5"   
## [389] "AA_ASAP90_ctrl_NP16-293_PFC_5"    "DA799_ASAP19_PD_NP16-160_PFC_5"  
## [391] "AA85_ASAP72_PD_NP19-23_PUT_5"     "AA_ASAP105_ctrl_NP16-293_SN_5"   
## [393] "AA_ASAP82_PD_NP21-217_PFC_5"      "AA_ASAP88_PD_NP21-217_PUT_5"     
## [395] "AA_ASAP100_ctrl_NP18-148_PUT_5"   "AA_ASAP109_PD_NP21-217_AMY_5"    
## [397] "DA430_ASAP9_PD_NP16-162_PFC_5"    "DA509_ASAP36_PD_NP19-16_PFC_5"   
## [399] "DA490_ASAP11_PD_P73_PFC_5"        "MJ_ASAP6_ctrl_NP16-164_SN_5"     
## [401] "AA_ASAP154_ctrl_NP21-04_PFC_5"    "AA86_ASAP73_PD_NP19-108_PUT_5"   
## [403] "AA_ASAP117_PD_NP22-55_PUT_5"      "AA_ASAP116_PD_NP22-55_PFC_5"     
## [405] "ASAP122_PD_NP19-91_AMY_5"         "AA_ASAP93_ctrl_NP16-293_PUT_5"   
## [407] "AA_ASAP91_ctrl_NP17-20_PFC_5"     "AA_ASAP96_ctrl_NP18-46_PUT_5"    
## [409] "AA_ASAP98_ctrl_NP16-119_PUT_5"    "DA473_ASAP38_PD_NP19-23_SN_5"    
## [411] "DA432_ASAP12_PD_P74_PFC_5"        "DA480_ASAP15_ctrl_NP16-21_PFC_5" 
## [413] "AA_ASAP153_ctrl_NP19-137_PFC_5"   "AA_ASAP108_ctrl_NP18-148_SN_5"   
## [415] "DA802_ASAP40_PD_NP19-23_AMY_5"    "DA775_ASAP22_PD_NP16-269_PFC_5"  
## [417] "DA779_ASAP33_PD_NP18-287_AMY_5"   "AA_ASAP149_PD_NP23-21_PUT_5"     
## [419] "AA82_ASAP68_PD_NP18-117_PUT_5"    "DA778_ASAP31_PD_NP18-117_AMY_5"  
## [421] "DA512_ASAP60_ctrl_NP19-45_AMY_5"  "AA_ASAP110_ctrl_NP16-119_AMY_5"  
## [423] "DA777_ASAP28_PD_NP17-191_PFC_5"   "MJ_ASAP14_ctrl_NP16-164_PFC_5"   
## [425] "AA_ASAP94_ctrl_NP17-20_PUT_5"     "AA_ASAP84_NP17-216_ctrl_PFC_5"   
## [427] "DA785_ASAP47_ctrl_NP17-256_PFC_5" "AA_ASAP92_ctrl_NP16-284_PUT_5"   
## [429] "DA784_ASAP46_ctrl_NP17-256_SN_5"  "DA808_ASAP41_PD_NP19-108_PFC_5"  
## [431] "AA_ASAP86_NP18-148_ctrl_PFC_5"    "AA_ASAP121_PD_NP17-232_AMY_5"    
## [433] "DA804_ASAP49_ctrl_NP18-159_PFC_5" "AA_ASAP119_PD_NP22-55_AMY_5"     
## [435] "AA_ASAP113_ctrl_NP18-148_AMY_5"   "AA_ASAP115_PD_NP21-208_AMY_5"    
## [437] "AA_ASAP151_PD_NP17-232_PFC_5"     "AA_ASAP104_ctrl_NP16-119_SN_5"   
## [439] "AA_ASAP131_PD_NP23-21_AMY_5"      "AA_ASAP140_PD_NP19-91_PUT_5"     
## [441] "DA791_ASAP50_ctrl_NP18-159_AMY_5" "AA_ASAP114_PD_NP21-57_AMY_5"     
## [443] "DA809_ASAP30_PD_NP18-117_PFC_5"   "DA782_ASAP41_PD_NP19-108_SN_5"   
## [445] "AA_ASAP99_ctrl_NP16-284_SN_5"     "AA_ASAP134_PD_NP19-91_SN_5"      
## [447] "AA_ASAP133_PD_NP17-232_SN_5"      "AA_ASAP139_PD_NP17-232_PUT_5"    
## [449] "AA_ASAP118_PD_NP22-55_SN_5"       "AA_ASAP112_ctrl_NP16-293_AMY_5"  
## [451] "AA_ASAP123_ctrl_NP19-218_AMY_5"   "AA_ASAP150_PD_NP16-285_PFC_5"    
## [453] "AA_ASAP128_PD_NP21-04_AMY_5"      "DA487_ASAP8_ctrl_PT231_SN_5"     
## [455] "DA429_ASAP1_PD_NP16-162_SN_5"     "DA796_ASAP57_ctrl_NP19-45_SN_5"  
## [457] "AA_ASAP141_ctrl_NP19-218_PUT_5"   "AA73_ASAP65_PD_NP16-269_PUT_5"   
## [459] "AA74_ASAP62_PD_NP16-140_PUT_5"    "DA811_ASAP18_PD_NP16-140_AMY_5"  
## [461] "AA79_ASAP64_PD_NP16-162_PUT_5"    "DA810_ASAP34_PD_NP18-304_PFC_5"  
## [463] "DA795_ASAP55_ctrl_NP19-37_PFC_5"  "AA_ASAP127_ctrl_NP19-218_SN_5"   
## [465] "DA475_ASAP2_PD_NP16-25_SN_5"      "AA_ASAP87_PD_NP21-208_PUT_5"     
## [467] "DA488_ASAP16_ctrl_PT231_PFC_5"    "AA_ASAP102_PD_NP21-208_SN_5"     
## [469] "DA431_ASAP4_PD_P74_SN_5"          "DA800_ASAP20_PD_NP16-160_AMY_5"  
## [471] "DA814_ASAP35_PD_NP18-304_AMY_5"   "AA78_ASAP63_PD_NP16-160_PUT_5"   
## [473] "AA_ASAP120_PD_NP16-285_AMY_5"     "DA428_ASAP13_ctrl_NP16-161_PFC_5"
## [475] "AA_ASAP138_PD_NP16-285_PUT_5"     "AA88_ASAP77_ctrl_NP19-36_PUT_5"  
## [477] "DA499_ASAP44_PD_NP19-255_PFC_5"   "AA_ASAP83_NP16-119_ctrl_PFC_5"   
## [479] "AA_ASAP132_PD_NP16-285_SN_5"      "AA_ASAP142_ctrl_NP22-37_PUT_5"   
## [481] "AA84_ASAP71_PD_NP19-16_PUT_5"     "AA_ASAP129_ctrl_NP22-37_SN_5"    
## [483] "AA_ASAP145_ctrl_NP19-218_PFC_5"   "AA89_ASAP78_ctrl_NP19-37_PUT_5"  
## [485] "AA76_ASAP74_PD_NP19-255_PUT_5"    "AA_ASAP124_ctrl_NP22-37_AMY_5"   
## [487] "AA_ASAP147_ctrl_NP22-37_PFC_5"    "AA83_ASAP69_PD_NP18-287_PUT_5"   
## [489] "AA_ASAP126_PD_NP19-137_AMY_5"     "ASAP155_ctrl_NP23-21_PFC_5"      
## [491] "DA511_ASAP21_PD_NP16-269_SN_5"    "DA805_ASAP56_ctrl_NP19-37_AMY_5" 
## [493] "DA433_ASAP5_ctrl_NP16-161_SN_5"   "DA476_ASAP10_PD_NP16-25_PFC_5"   
## [495] "DA792_ASAP51_ctrl_NP19-36_SN_5"   "AA_ASAP137_PD_NP23-21_SN_5"      
## [497] "DA806_ASAP58_ctrl_NP19-45_PFC_5"  "AA71_ASAP70_PD_NP18-304_PUT_5"   
## [499] "AA81_ASAP67_PD_NP17-191_PUT_5"    "DA813_ASAP17_PD_NP16-140_PFC_5"  
## [501] "DA479_ASAP7_ctrl_NP16-21_SN_5"    "DA801_ASAP53_ctrl_NP19-36_AMY_5" 
## [503] "DA793_ASAP53_ctrl_NP19-36_AMY_5"  "DA815_ASAP37_PD_NP19-16_AMY_5"   
## [505] "DA780_ASAP37_PD_NP19-16_AMY_5"    "DA807_ASAP29_PD_NP17-191_AMY_5"  
## [507] "AA_ASAP135_PD_NP19-137_SN_5"      "AA_ASAP144_PD_NP19-137_PUT_5"    
## [509] "DA474_ASAP24_PD_NP16-25_AMY_5"    "DA794_ASAP54_ctrl_NP19-37_SN_5"  
## [511] "AA77_ASAP61_PD_NP16-25_PUT_5"     "AA_ASAP146_PD_NP21-04_PUT_5"     
## [513] "AA_ASAP136_PD_NP21-04_SN_5"       "DA791_ASAP50_ctrl_NP18-159_AMY_4"
## [515] "AA_ASAP112_ctrl_NP16-293_AMY_4"   "DA512_ASAP60_ctrl_NP19-45_AMY_4" 
## [517] "AA_ASAP115_PD_NP21-208_AMY_4"     "DA802_ASAP40_PD_NP19-23_AMY_4"   
## [519] "AA_ASAP86_NP18-148_ctrl_PFC_4"    "AA_ASAP145_ctrl_NP19-218_PFC_4"  
## [521] "AA_ASAP89_ctrl_NP16-284_PFC_4"    "AA_ASAP90_ctrl_NP16-293_PFC_4"   
## [523] "MJ_ASAP14_ctrl_NP16-164_PFC_4"    "DA480_ASAP15_ctrl_NP16-21_PFC_4" 
## [525] "AA_ASAP151_PD_NP17-232_PFC_4"     "ASAP155_ctrl_NP23-21_PFC_4"      
## [527] "DA775_ASAP22_PD_NP16-269_PFC_4"   "AA_ASAP116_PD_NP22-55_PFC_4"     
## [529] "AA_ASAP82_PD_NP21-217_PFC_4"      "DA430_ASAP9_PD_NP16-162_PFC_4"   
## [531] "DA490_ASAP11_PD_P73_PFC_4"        "AA89_ASAP78_ctrl_NP19-37_PUT_4"  
## [533] "AA_ASAP98_ctrl_NP16-119_PUT_4"    "AA_ASAP94_ctrl_NP17-20_PUT_4"    
## [535] "AA_ASAP138_PD_NP16-285_PUT_4"     "AA84_ASAP71_PD_NP19-16_PUT_4"    
## [537] "AA85_ASAP72_PD_NP19-23_PUT_4"     "AA_ASAP87_PD_NP21-208_PUT_4"     
## [539] "AA_ASAP88_PD_NP21-217_PUT_4"      "AA79_ASAP64_PD_NP16-162_PUT_4"   
## [541] "AA73_ASAP65_PD_NP16-269_PUT_4"    "AA71_ASAP70_PD_NP18-304_PUT_4"   
## [543] "AA_ASAP108_ctrl_NP18-148_SN_4"    "DA433_ASAP5_ctrl_NP16-161_SN_4"  
## [545] "AA_ASAP134_PD_NP19-91_SN_4"       "DA782_ASAP41_PD_NP19-108_SN_4"   
## [547] "AA_ASAP101_PD_NP21-57_SN_4"       "DA473_ASAP38_PD_NP19-23_SN_4"    
## [549] "AA_ASAP103_PD_NP21-217_SN_4"      "AA_ASAP119_PD_NP22-55_AMY_4"     
## [551] "AA87_ASAP76_ctrl_NP18-159_PUT_4"  "AA76_ASAP74_PD_NP19-255_PUT_4"   
## [553] "AA_ASAP141_ctrl_NP19-218_PUT_4"   "AA_ASAP100_ctrl_NP18-148_PUT_4"  
## [555] "DA488_ASAP16_ctrl_PT231_PFC_4"    "DA432_ASAP12_PD_P74_PFC_4"       
## [557] "AA_ASAP129_ctrl_NP22-37_SN_4"     "DA808_ASAP41_PD_NP19-108_PFC_4"  
## [559] "AA_ASAP140_PD_NP19-91_PUT_4"      "DA806_ASAP58_ctrl_NP19-45_PFC_4" 
## [561] "AA_ASAP133_PD_NP17-232_SN_4"      "AA_ASAP117_PD_NP22-55_PUT_4"     
## [563] "AA_ASAP80_PD_NP21-57_PFC_4"       "AA_ASAP113_ctrl_NP18-148_AMY_4"  
## [565] "AA_ASAP96_ctrl_NP18-46_PUT_4"     "DA804_ASAP49_ctrl_NP18-159_PFC_4"
## [567] "AA_ASAP126_PD_NP19-137_AMY_4"     "AA_ASAP118_PD_NP22-55_SN_4"      
## [569] "DA783_ASAP45_PD_NP19-255_AMY_4"   "DA811_ASAP18_PD_NP16-140_AMY_4"  
## [571] "AA_ASAP114_PD_NP21-57_AMY_4"      "DA793_ASAP53_ctrl_NP19-36_AMY_4" 
## [573] "AA_ASAP123_ctrl_NP19-218_AMY_4"   "AA_ASAP110_ctrl_NP16-119_AMY_4"  
## [575] "AA_ASAP97_PD_NP21-57_PUT_4"       "AA_ASAP152_PD_NP19-91_PFC_4"     
## [577] "DA499_ASAP44_PD_NP19-255_PFC_4"   "AA_ASAP104_ctrl_NP16-119_SN_4"   
## [579] "DA489_ASAP3_PD_P73_SN_4"          "AA77_ASAP61_PD_NP16-25_PUT_4"    
## [581] "DA487_ASAP8_ctrl_PT231_SN_4"      "AA_ASAP83_NP16-119_ctrl_PFC_4"   
## [583] "DA476_ASAP10_PD_NP16-25_PFC_4"    "AA_ASAP102_PD_NP21-208_SN_4"     
## [585] "AA83_ASAP69_PD_NP18-287_PUT_4"    "DA792_ASAP51_ctrl_NP19-36_SN_4"  
## [587] "AA_ASAP131_PD_NP23-21_AMY_4"      "AA_ASAP144_PD_NP19-137_PUT_4"    
## [589] "DA431_ASAP4_PD_P74_SN_4"          "DA794_ASAP54_ctrl_NP19-37_SN_4"  
## [591] "DA795_ASAP55_ctrl_NP19-37_PFC_4"  "AA_ASAP127_ctrl_NP19-218_SN_4"   
## [593] "DA801_ASAP53_ctrl_NP19-36_AMY_4"  "AA_ASAP135_PD_NP19-137_SN_4"     
## [595] "DA511_ASAP21_PD_NP16-269_SN_4"    "DA805_ASAP56_ctrl_NP19-37_AMY_4" 
## [597] "AA74_ASAP62_PD_NP16-140_PUT_4"    "DA428_ASAP13_ctrl_NP16-161_PFC_4"
## [599] "DA474_ASAP24_PD_NP16-25_AMY_4"    "AA_ASAP137_PD_NP23-21_SN_4"      
## [601] "DA807_ASAP29_PD_NP17-191_AMY_4"   "DA475_ASAP2_PD_NP16-25_SN_4"     
## [603] "DA429_ASAP1_PD_NP16-162_SN_4"     "MJ_ASAP6_ctrl_NP16-164_SN_4"     
## [605] "AA81_ASAP67_PD_NP17-191_PUT_4"    "DA778_ASAP31_PD_NP18-117_AMY_4"  
## [607] "AA_ASAP152_PD_NP19-91_PFC_6"      "AA_ASAP89_ctrl_NP16-284_PFC_6"   
## [609] "DA785_ASAP47_ctrl_NP17-256_PFC_6" "MJ_ASAP14_ctrl_NP16-164_PFC_6"   
## [611] "DA428_ASAP13_ctrl_NP16-161_PFC_6" "AA_ASAP137_PD_NP23-21_SN_6"      
## [613] "AA_ASAP123_ctrl_NP19-218_AMY_6"   "DA792_ASAP51_ctrl_NP19-36_SN_6"  
## [615] "AA_ASAP133_PD_NP17-232_SN_7"      "AA_ASAP108_ctrl_NP18-148_SN_7"   
## [617] "AA_ASAP137_PD_NP23-21_SN_7"      
## 
## $order_rows
## [1] NA

asap_heatmap_snRNA(region = c("PFC", "PUT", "AMY", "SN"), 
                   tes = L1s_notexpressed, 
                   return_df = F, 
                   breaks = seq(0,15,length.out = 52),
                   data = TE_data, 
                   group_cols = c("celltype"), 
                   order_cols_groups = order_cols_celltype,
                   title = "Not expressed L1s: >50 nuclei pseudobulks", data_TE_annotation = data_TE_annotation)

## $heatmap
## 
## $order_cols
##   [1] "AA_ASAP80_PD_NP21-57_PFC_0"       "AA_ASAP97_PD_NP21-57_PUT_0"      
##   [3] "DA780_ASAP37_PD_NP19-16_AMY_0"    "AA82_ASAP68_PD_NP18-117_PUT_0"   
##   [5] "AA79_ASAP64_PD_NP16-162_PUT_0"    "AA_ASAP110_ctrl_NP16-119_AMY_0"  
##   [7] "DA793_ASAP53_ctrl_NP19-36_AMY_0"  "AA84_ASAP71_PD_NP19-16_PUT_0"    
##   [9] "DA806_ASAP58_ctrl_NP19-45_PFC_0"  "DA777_ASAP28_PD_NP17-191_PFC_0"  
##  [11] "DA795_ASAP55_ctrl_NP19-37_PFC_0"  "DA476_ASAP10_PD_NP16-25_PFC_0"   
##  [13] "DA430_ASAP9_PD_NP16-162_PFC_0"    "AA_ASAP82_PD_NP21-217_PFC_0"     
##  [15] "AA_ASAP89_ctrl_NP16-284_PFC_0"    "ASAP155_ctrl_NP23-21_PFC_0"      
##  [17] "AA_ASAP152_PD_NP19-91_PFC_0"      "DA480_ASAP15_ctrl_NP16-21_PFC_0" 
##  [19] "AA_ASAP90_ctrl_NP16-293_PFC_0"    "DA428_ASAP13_ctrl_NP16-161_PFC_0"
##  [21] "DA805_ASAP56_ctrl_NP19-37_AMY_0"  "DA490_ASAP11_PD_P73_PFC_0"       
##  [23] "AA_ASAP100_ctrl_NP18-148_PUT_0"   "AA_ASAP85_NP18-46_ctrl_PFC_0"    
##  [25] "DA811_ASAP18_PD_NP16-140_AMY_0"   "AA_ASAP145_ctrl_NP19-218_PFC_0"  
##  [27] "AA_ASAP86_NP18-148_ctrl_PFC_0"    "DA432_ASAP12_PD_P74_PFC_0"       
##  [29] "AA87_ASAP76_ctrl_NP18-159_PUT_0"  "AA_ASAP81_PD_NP21-208_PFC_0"     
##  [31] "AA_ASAP98_ctrl_NP16-119_PUT_0"    "AA_ASAP91_ctrl_NP17-20_PFC_0"    
##  [33] "MJ_ASAP14_ctrl_NP16-164_PFC_0"    "AA74_ASAP62_PD_NP16-140_PUT_0"   
##  [35] "AA_ASAP138_PD_NP16-285_PUT_0"     "AA_ASAP151_PD_NP17-232_PFC_0"    
##  [37] "AA_ASAP116_PD_NP22-55_PFC_0"      "AA_ASAP114_PD_NP21-57_AMY_0"     
##  [39] "DA509_ASAP36_PD_NP19-16_PFC_0"    "DA810_ASAP34_PD_NP18-304_PFC_0"  
##  [41] "DA474_ASAP24_PD_NP16-25_AMY_0"    "AA_ASAP83_NP16-119_ctrl_PFC_0"   
##  [43] "AA_ASAP141_ctrl_NP19-218_PUT_0"   "DA809_ASAP30_PD_NP18-117_PFC_0"  
##  [45] "AA_ASAP153_ctrl_NP19-137_PFC_0"   "DA778_ASAP31_PD_NP18-117_AMY_0"  
##  [47] "DA488_ASAP16_ctrl_PT231_PFC_0"    "DA499_ASAP44_PD_NP19-255_PFC_0"  
##  [49] "DA783_ASAP45_PD_NP19-255_AMY_0"   "DA791_ASAP50_ctrl_NP18-159_AMY_0"
##  [51] "AA_ASAP115_PD_NP21-208_AMY_0"     "DA804_ASAP49_ctrl_NP18-159_PFC_0"
##  [53] "DA813_ASAP17_PD_NP16-140_PFC_0"   "DA775_ASAP22_PD_NP16-269_PFC_0"  
##  [55] "AA71_ASAP70_PD_NP18-304_PUT_0"    "DA802_ASAP40_PD_NP19-23_AMY_0"   
##  [57] "DA775_ASAP22_PD_NP16-269_PFC_1"   "DA802_ASAP40_PD_NP19-23_AMY_1"   
##  [59] "AA_ASAP131_PD_NP23-21_AMY_1"      "AA_ASAP123_ctrl_NP19-218_AMY_1"  
##  [61] "DA430_ASAP9_PD_NP16-162_PFC_1"    "DA778_ASAP31_PD_NP18-117_AMY_1"  
##  [63] "AA_ASAP117_PD_NP22-55_PUT_1"      "AA_ASAP121_PD_NP17-232_AMY_1"    
##  [65] "AA_ASAP110_ctrl_NP16-119_AMY_1"   "DA805_ASAP56_ctrl_NP19-37_AMY_1" 
##  [67] "DA777_ASAP28_PD_NP17-191_PFC_1"   "DA512_ASAP60_ctrl_NP19-45_AMY_1" 
##  [69] "DA487_ASAP8_ctrl_PT231_SN_1"      "DA809_ASAP30_PD_NP18-117_PFC_1"  
##  [71] "DA480_ASAP15_ctrl_NP16-21_PFC_1"  "AA_ASAP144_PD_NP19-137_PUT_1"    
##  [73] "AA_ASAP126_PD_NP19-137_AMY_1"     "AA_ASAP118_PD_NP22-55_SN_1"      
##  [75] "AA_ASAP137_PD_NP23-21_SN_1"       "AA_ASAP129_ctrl_NP22-37_SN_1"    
##  [77] "AA71_ASAP70_PD_NP18-304_PUT_1"    "AA79_ASAP64_PD_NP16-162_PUT_1"   
##  [79] "AA74_ASAP62_PD_NP16-140_PUT_1"    "AA_ASAP100_ctrl_NP18-148_PUT_1"  
##  [81] "AA_ASAP92_ctrl_NP16-284_PUT_1"    "AA_ASAP116_PD_NP22-55_PFC_1"     
##  [83] "MJ_ASAP14_ctrl_NP16-164_PFC_1"    "AA_ASAP89_ctrl_NP16-284_PFC_1"   
##  [85] "AA_ASAP85_NP18-46_ctrl_PFC_1"     "AA_ASAP119_PD_NP22-55_AMY_1"     
##  [87] "AA_ASAP109_PD_NP21-217_AMY_1"     "AA_ASAP124_ctrl_NP22-37_AMY_1"   
##  [89] "AA_ASAP128_PD_NP21-04_AMY_1"      "DA428_ASAP13_ctrl_NP16-161_PFC_1"
##  [91] "DA490_ASAP11_PD_P73_PFC_1"        "DA476_ASAP10_PD_NP16-25_PFC_1"   
##  [93] "AA_ASAP83_NP16-119_ctrl_PFC_1"    "DA810_ASAP34_PD_NP18-304_PFC_1"  
##  [95] "DA792_ASAP51_ctrl_NP19-36_SN_1"   "DA432_ASAP12_PD_P74_PFC_1"       
##  [97] "DA474_ASAP24_PD_NP16-25_AMY_1"    "DA811_ASAP18_PD_NP16-140_AMY_1"  
##  [99] "AA_ASAP90_ctrl_NP16-293_PFC_1"    "AA_ASAP88_PD_NP21-217_PUT_1"     
## [101] "DA783_ASAP45_PD_NP19-255_AMY_1"   "DA780_ASAP37_PD_NP19-16_AMY_1"   
## [103] "AA_ASAP82_PD_NP21-217_PFC_1"      "AA_ASAP115_PD_NP21-208_AMY_1"    
## [105] "AA_ASAP81_PD_NP21-208_PFC_1"      "AA_ASAP86_NP18-148_ctrl_PFC_1"   
## [107] "DA488_ASAP16_ctrl_PT231_PFC_1"    "ASAP155_ctrl_NP23-21_PFC_1"      
## [109] "DA509_ASAP36_PD_NP19-16_PFC_1"    "AA_ASAP151_PD_NP17-232_PFC_1"    
## [111] "AA_ASAP91_ctrl_NP17-20_PFC_1"     "DA795_ASAP55_ctrl_NP19-37_PFC_1" 
## [113] "AA_ASAP145_ctrl_NP19-218_PFC_1"   "AA87_ASAP76_ctrl_NP18-159_PUT_1" 
## [115] "AA_ASAP152_PD_NP19-91_PFC_1"      "AA_ASAP113_ctrl_NP18-148_AMY_1"  
## [117] "AA_ASAP80_PD_NP21-57_PFC_1"       "DA801_ASAP53_ctrl_NP19-36_AMY_1" 
## [119] "AA_ASAP114_PD_NP21-57_AMY_1"      "AA84_ASAP71_PD_NP19-16_PUT_1"    
## [121] "AA_ASAP139_PD_NP17-232_PUT_1"     "AA_ASAP153_ctrl_NP19-137_PFC_1"  
## [123] "DA804_ASAP49_ctrl_NP18-159_PFC_1" "DA806_ASAP58_ctrl_NP19-45_PFC_1" 
## [125] "DA499_ASAP44_PD_NP19-255_PFC_1"   "DA793_ASAP53_ctrl_NP19-36_AMY_1" 
## [127] "DA791_ASAP50_ctrl_NP18-159_AMY_1" "AA_ASAP87_PD_NP21-208_PUT_1"     
## [129] "DA488_ASAP16_ctrl_PT231_PFC_2"    "DA489_ASAP3_PD_P73_SN_2"         
## [131] "DA805_ASAP56_ctrl_NP19-37_AMY_2"  "DA511_ASAP21_PD_NP16-269_SN_2"   
## [133] "AA_ASAP131_PD_NP23-21_AMY_2"      "AA_ASAP128_PD_NP21-04_AMY_2"     
## [135] "DA811_ASAP18_PD_NP16-140_AMY_2"   "AA_ASAP109_PD_NP21-217_AMY_2"    
## [137] "AA_ASAP119_PD_NP22-55_AMY_2"      "AA_ASAP84_NP17-216_ctrl_PFC_2"   
## [139] "AA_ASAP145_ctrl_NP19-218_PFC_2"   "AA_ASAP89_ctrl_NP16-284_PFC_2"   
## [141] "AA_ASAP91_ctrl_NP17-20_PFC_2"     "AA_ASAP153_ctrl_NP19-137_PFC_2"  
## [143] "DA499_ASAP44_PD_NP19-255_PFC_2"   "DA476_ASAP10_PD_NP16-25_PFC_2"   
## [145] "DA490_ASAP11_PD_P73_PFC_2"        "AA88_ASAP77_ctrl_NP19-36_PUT_2"  
## [147] "AA89_ASAP78_ctrl_NP19-37_PUT_2"   "AA_ASAP96_ctrl_NP18-46_PUT_2"    
## [149] "AA82_ASAP68_PD_NP18-117_PUT_2"    "AA85_ASAP72_PD_NP19-23_PUT_2"    
## [151] "AA_ASAP117_PD_NP22-55_PUT_2"      "AA76_ASAP74_PD_NP19-255_PUT_2"   
## [153] "AA_ASAP127_ctrl_NP19-218_SN_2"    "AA_ASAP129_ctrl_NP22-37_SN_2"    
## [155] "DA784_ASAP46_ctrl_NP17-256_SN_2"  "DA792_ASAP51_ctrl_NP19-36_SN_2"  
## [157] "AA_ASAP99_ctrl_NP16-284_SN_2"     "AA_ASAP108_ctrl_NP18-148_SN_2"   
## [159] "DA433_ASAP5_ctrl_NP16-161_SN_2"   "MJ_ASAP6_ctrl_NP16-164_SN_2"     
## [161] "DA479_ASAP7_ctrl_NP16-21_SN_2"    "AA_ASAP132_PD_NP16-285_SN_2"     
## [163] "AA_ASAP134_PD_NP19-91_SN_2"       "AA_ASAP135_PD_NP19-137_SN_2"     
## [165] "DA782_ASAP41_PD_NP19-108_SN_2"    "AA_ASAP101_PD_NP21-57_SN_2"      
## [167] "DA475_ASAP2_PD_NP16-25_SN_2"      "DA431_ASAP4_PD_P74_SN_2"         
## [169] "DA783_ASAP45_PD_NP19-255_AMY_2"   "ASAP122_PD_NP19-91_AMY_2"        
## [171] "AA_ASAP121_PD_NP17-232_AMY_2"     "AA_ASAP82_PD_NP21-217_PFC_2"     
## [173] "AA81_ASAP67_PD_NP17-191_PUT_2"    "AA_ASAP116_PD_NP22-55_PFC_2"     
## [175] "AA_ASAP118_PD_NP22-55_SN_2"       "DA432_ASAP12_PD_P74_PFC_2"       
## [177] "AA83_ASAP69_PD_NP18-287_PUT_2"    "AA_ASAP88_PD_NP21-217_PUT_2"     
## [179] "DA794_ASAP54_ctrl_NP19-37_SN_2"   "AA_ASAP86_NP18-148_ctrl_PFC_2"   
## [181] "AA_ASAP126_PD_NP19-137_AMY_2"     "AA_ASAP152_PD_NP19-91_PFC_2"     
## [183] "DA480_ASAP15_ctrl_NP16-21_PFC_2"  "AA_ASAP154_ctrl_NP21-04_PFC_2"   
## [185] "AA_ASAP140_PD_NP19-91_PUT_2"      "AA_ASAP137_PD_NP23-21_SN_2"      
## [187] "DA807_ASAP29_PD_NP17-191_AMY_2"   "AA_ASAP103_PD_NP21-217_SN_2"     
## [189] "DA796_ASAP57_ctrl_NP19-45_SN_2"   "AA_ASAP104_ctrl_NP16-119_SN_2"   
## [191] "AA_ASAP113_ctrl_NP18-148_AMY_2"   "DA804_ASAP49_ctrl_NP18-159_PFC_2"
## [193] "AA84_ASAP71_PD_NP19-16_PUT_2"     "AA_ASAP102_PD_NP21-208_SN_2"     
## [195] "AA_ASAP150_PD_NP16-285_PFC_2"     "MJ_ASAP14_ctrl_NP16-164_PFC_2"   
## [197] "AA_ASAP120_PD_NP16-285_AMY_2"     "AA_ASAP81_PD_NP21-208_PFC_2"     
## [199] "DA429_ASAP1_PD_NP16-162_SN_2"     "DA778_ASAP31_PD_NP18-117_AMY_2"  
## [201] "DA780_ASAP37_PD_NP19-16_AMY_2"    "DA806_ASAP58_ctrl_NP19-45_PFC_2" 
## [203] "AA_ASAP80_PD_NP21-57_PFC_2"       "DA802_ASAP40_PD_NP19-23_AMY_2"   
## [205] "DA775_ASAP22_PD_NP16-269_PFC_2"   "AA77_ASAP61_PD_NP16-25_PUT_2"    
## [207] "AA_ASAP105_ctrl_NP16-293_SN_2"    "DA808_ASAP41_PD_NP19-108_PFC_2"  
## [209] "AA_ASAP123_ctrl_NP19-218_AMY_2"   "AA_ASAP112_ctrl_NP16-293_AMY_2"  
## [211] "AA_ASAP133_PD_NP17-232_SN_2"      "DA814_ASAP35_PD_NP18-304_AMY_2"  
## [213] "DA791_ASAP50_ctrl_NP18-159_AMY_2" "AA_ASAP94_ctrl_NP17-20_PUT_2"    
## [215] "AA_ASAP124_ctrl_NP22-37_AMY_2"    "AA86_ASAP73_PD_NP19-108_PUT_2"   
## [217] "AA_ASAP92_ctrl_NP16-284_PUT_2"    "ASAP155_ctrl_NP23-21_PFC_2"      
## [219] "DA428_ASAP13_ctrl_NP16-161_PFC_2" "AA71_ASAP70_PD_NP18-304_PUT_2"   
## [221] "DA785_ASAP47_ctrl_NP17-256_PFC_2" "AA73_ASAP65_PD_NP16-269_PUT_2"   
## [223] "AA_ASAP87_PD_NP21-208_PUT_2"      "AA_ASAP141_ctrl_NP19-218_PUT_2"  
## [225] "AA_ASAP139_PD_NP17-232_PUT_2"     "AA_ASAP146_PD_NP21-04_PUT_2"     
## [227] "AA_ASAP138_PD_NP16-285_PUT_2"     "AA74_ASAP62_PD_NP16-140_PUT_2"   
## [229] "DA810_ASAP34_PD_NP18-304_PFC_2"   "AA_ASAP97_PD_NP21-57_PUT_2"      
## [231] "DA430_ASAP9_PD_NP16-162_PFC_2"    "DA474_ASAP24_PD_NP16-25_AMY_2"   
## [233] "DA801_ASAP53_ctrl_NP19-36_AMY_2"  "AA_ASAP110_ctrl_NP16-119_AMY_2"  
## [235] "DA809_ASAP30_PD_NP18-117_PFC_2"   "AA_ASAP93_ctrl_NP16-293_PUT_2"   
## [237] "AA87_ASAP76_ctrl_NP18-159_PUT_2"  "AA_ASAP114_PD_NP21-57_AMY_2"     
## [239] "AA_ASAP151_PD_NP17-232_PFC_2"     "AA_ASAP115_PD_NP21-208_AMY_2"    
## [241] "AA79_ASAP64_PD_NP16-162_PUT_2"    "AA_ASAP83_NP16-119_ctrl_PFC_2"   
## [243] "DA473_ASAP38_PD_NP19-23_SN_2"     "DA793_ASAP53_ctrl_NP19-36_AMY_2" 
## [245] "AA_ASAP100_ctrl_NP18-148_PUT_2"   "DA512_ASAP60_ctrl_NP19-45_AMY_2" 
## [247] "DA795_ASAP55_ctrl_NP19-37_PFC_2"  "DA509_ASAP36_PD_NP19-16_PFC_2"   
## [249] "AA_ASAP90_ctrl_NP16-293_PFC_2"    "AA_ASAP144_PD_NP19-137_PUT_2"    
## [251] "DA487_ASAP8_ctrl_PT231_SN_2"      "AA_ASAP98_ctrl_NP16-119_PUT_2"   
## [253] "DA803_ASAP48_ctrl_NP17-256_AMY_3" "AA_ASAP111_ctrl_NP16-284_AMY_3"  
## [255] "AA_ASAP121_PD_NP17-232_AMY_3"     "AA_ASAP131_PD_NP23-21_AMY_3"     
## [257] "DA783_ASAP45_PD_NP19-255_AMY_3"   "AA_ASAP115_PD_NP21-208_AMY_3"    
## [259] "AA_ASAP84_NP17-216_ctrl_PFC_3"    "AA_ASAP86_NP18-148_ctrl_PFC_3"   
## [261] "DA785_ASAP47_ctrl_NP17-256_PFC_3" "AA_ASAP91_ctrl_NP17-20_PFC_3"    
## [263] "DA480_ASAP15_ctrl_NP16-21_PFC_3"  "DA488_ASAP16_ctrl_PT231_PFC_3"   
## [265] "AA_ASAP150_PD_NP16-285_PFC_3"     "AA_ASAP154_ctrl_NP21-04_PFC_3"   
## [267] "ASAP155_ctrl_NP23-21_PFC_3"       "DA777_ASAP28_PD_NP17-191_PFC_3"  
## [269] "AA_ASAP116_PD_NP22-55_PFC_3"      "AA_ASAP82_PD_NP21-217_PFC_3"     
## [271] "DA430_ASAP9_PD_NP16-162_PFC_3"    "DA490_ASAP11_PD_P73_PFC_3"       
## [273] "DA432_ASAP12_PD_P74_PFC_3"        "DA509_ASAP36_PD_NP19-16_PFC_3"   
## [275] "AA_ASAP141_ctrl_NP19-218_PUT_3"   "AA_ASAP142_ctrl_NP22-37_PUT_3"   
## [277] "AA_ASAP100_ctrl_NP18-148_PUT_3"   "AA_ASAP93_ctrl_NP16-293_PUT_3"   
## [279] "AA_ASAP138_PD_NP16-285_PUT_3"     "AA_ASAP139_PD_NP17-232_PUT_3"    
## [281] "AA_ASAP140_PD_NP19-91_PUT_3"      "AA_ASAP144_PD_NP19-137_PUT_3"    
## [283] "AA_ASAP149_PD_NP23-21_PUT_3"      "AA81_ASAP67_PD_NP17-191_PUT_3"   
## [285] "AA82_ASAP68_PD_NP18-117_PUT_3"    "AA86_ASAP73_PD_NP19-108_PUT_3"   
## [287] "AA85_ASAP72_PD_NP19-23_PUT_3"     "AA_ASAP117_PD_NP22-55_PUT_3"     
## [289] "AA74_ASAP62_PD_NP16-140_PUT_3"    "AA73_ASAP65_PD_NP16-269_PUT_3"   
## [291] "AA76_ASAP74_PD_NP19-255_PUT_3"    "AA_ASAP129_ctrl_NP22-37_SN_3"    
## [293] "AA_ASAP99_ctrl_NP16-284_SN_3"     "AA_ASAP108_ctrl_NP18-148_SN_3"   
## [295] "DA433_ASAP5_ctrl_NP16-161_SN_3"   "MJ_ASAP6_ctrl_NP16-164_SN_3"     
## [297] "AA_ASAP132_PD_NP16-285_SN_3"      "AA_ASAP136_PD_NP21-04_SN_3"      
## [299] "AA_ASAP137_PD_NP23-21_SN_3"       "DA782_ASAP41_PD_NP19-108_SN_3"   
## [301] "AA_ASAP103_PD_NP21-217_SN_3"      "DA429_ASAP1_PD_NP16-162_SN_3"    
## [303] "DA475_ASAP2_PD_NP16-25_SN_3"      "DA431_ASAP4_PD_P74_SN_3"         
## [305] "DA791_ASAP50_ctrl_NP18-159_AMY_3" "DA804_ASAP49_ctrl_NP18-159_PFC_3"
## [307] "DA473_ASAP38_PD_NP19-23_SN_3"     "AA_ASAP97_PD_NP21-57_PUT_3"      
## [309] "AA89_ASAP78_ctrl_NP19-37_PUT_3"   "DA479_ASAP7_ctrl_NP16-21_SN_3"   
## [311] "DA802_ASAP40_PD_NP19-23_AMY_3"    "DA794_ASAP54_ctrl_NP19-37_SN_3"  
## [313] "AA_ASAP151_PD_NP17-232_PFC_3"     "AA_ASAP92_ctrl_NP16-284_PUT_3"   
## [315] "AA_ASAP146_PD_NP21-04_PUT_3"      "DA807_ASAP29_PD_NP17-191_AMY_3"  
## [317] "DA487_ASAP8_ctrl_PT231_SN_3"      "AA_ASAP98_ctrl_NP16-119_PUT_3"   
## [319] "AA_ASAP87_PD_NP21-208_PUT_3"      "AA84_ASAP71_PD_NP19-16_PUT_3"    
## [321] "AA_ASAP119_PD_NP22-55_AMY_3"      "AA83_ASAP69_PD_NP18-287_PUT_3"   
## [323] "DA796_ASAP57_ctrl_NP19-45_SN_3"   "AA_ASAP89_ctrl_NP16-284_PFC_3"   
## [325] "AA88_ASAP77_ctrl_NP19-36_PUT_3"   "AA_ASAP102_PD_NP21-208_SN_3"     
## [327] "AA79_ASAP64_PD_NP16-162_PUT_3"    "AA_ASAP83_NP16-119_ctrl_PFC_3"   
## [329] "DA809_ASAP30_PD_NP18-117_PFC_3"   "AA_ASAP88_PD_NP21-217_PUT_3"     
## [331] "AA_ASAP124_ctrl_NP22-37_AMY_3"    "AA_ASAP135_PD_NP19-137_SN_3"     
## [333] "MJ_ASAP14_ctrl_NP16-164_PFC_3"    "AA_ASAP145_ctrl_NP19-218_PFC_3"  
## [335] "AA_ASAP118_PD_NP22-55_SN_3"       "AA87_ASAP76_ctrl_NP18-159_PUT_3" 
## [337] "AA_ASAP96_ctrl_NP18-46_PUT_3"     "DA784_ASAP46_ctrl_NP17-256_SN_3" 
## [339] "AA_ASAP80_PD_NP21-57_PFC_3"       "DA806_ASAP58_ctrl_NP19-45_PFC_3" 
## [341] "DA476_ASAP10_PD_NP16-25_PFC_3"    "DA512_ASAP60_ctrl_NP19-45_AMY_3" 
## [343] "ASAP122_PD_NP19-91_AMY_3"         "AA_ASAP112_ctrl_NP16-293_AMY_3"  
## [345] "AA_ASAP109_PD_NP21-217_AMY_3"     "DA775_ASAP22_PD_NP16-269_PFC_3"  
## [347] "AA_ASAP105_ctrl_NP16-293_SN_3"    "AA_ASAP104_ctrl_NP16-119_SN_3"   
## [349] "AA_ASAP120_PD_NP16-285_AMY_3"     "AA_ASAP134_PD_NP19-91_SN_3"      
## [351] "AA_ASAP90_ctrl_NP16-293_PFC_3"    "AA_ASAP123_ctrl_NP19-218_AMY_3"  
## [353] "DA805_ASAP56_ctrl_NP19-37_AMY_3"  "DA792_ASAP51_ctrl_NP19-36_SN_3"  
## [355] "AA77_ASAP61_PD_NP16-25_PUT_3"     "DA795_ASAP55_ctrl_NP19-37_PFC_3" 
## [357] "DA793_ASAP53_ctrl_NP19-36_AMY_3"  "DA780_ASAP37_PD_NP19-16_AMY_3"   
## [359] "DA778_ASAP31_PD_NP18-117_AMY_3"   "AA71_ASAP70_PD_NP18-304_PUT_3"   
## [361] "AA_ASAP114_PD_NP21-57_AMY_3"      "AA_ASAP113_ctrl_NP18-148_AMY_3"  
## [363] "AA_ASAP128_PD_NP21-04_AMY_3"      "AA_ASAP101_PD_NP21-57_SN_3"      
## [365] "AA_ASAP94_ctrl_NP17-20_PUT_3"     "DA428_ASAP13_ctrl_NP16-161_PFC_3"
## [367] "AA_ASAP133_PD_NP17-232_SN_3"      "DA474_ASAP24_PD_NP16-25_AMY_3"   
## [369] "DA811_ASAP18_PD_NP16-140_AMY_3"   "DA810_ASAP34_PD_NP18-304_PFC_3"  
## [371] "DA489_ASAP3_PD_P73_SN_3"          "DA499_ASAP44_PD_NP19-255_PFC_3"  
## [373] "AA_ASAP152_PD_NP19-91_PFC_3"      "AA_ASAP127_ctrl_NP19-218_SN_3"   
## [375] "DA511_ASAP21_PD_NP16-269_SN_3"    "DA801_ASAP53_ctrl_NP19-36_AMY_3" 
## [377] "AA_ASAP110_ctrl_NP16-119_AMY_3"   "DA783_ASAP45_PD_NP19-255_AMY_5"  
## [379] "DA801_ASAP53_ctrl_NP19-36_AMY_5"  "DA479_ASAP7_ctrl_NP16-21_SN_5"   
## [381] "AA_ASAP112_ctrl_NP16-293_AMY_5"   "AA89_ASAP78_ctrl_NP19-37_PUT_5"  
## [383] "DA429_ASAP1_PD_NP16-162_SN_5"     "AA_ASAP119_PD_NP22-55_AMY_5"     
## [385] "AA88_ASAP77_ctrl_NP19-36_PUT_5"   "AA_ASAP120_PD_NP16-285_AMY_5"    
## [387] "DA779_ASAP33_PD_NP18-287_AMY_5"   "DA791_ASAP50_ctrl_NP18-159_AMY_5"
## [389] "MJ_ASAP6_ctrl_NP16-164_SN_5"      "AA_ASAP132_PD_NP16-285_SN_5"     
## [391] "AA_ASAP153_ctrl_NP19-137_PFC_5"   "DA474_ASAP24_PD_NP16-25_AMY_5"   
## [393] "AA_ASAP142_ctrl_NP22-37_PUT_5"    "AA_ASAP86_NP18-148_ctrl_PFC_5"   
## [395] "AA_ASAP117_PD_NP22-55_PUT_5"      "DA775_ASAP22_PD_NP16-269_PFC_5"  
## [397] "AA_ASAP90_ctrl_NP16-293_PFC_5"    "AA83_ASAP69_PD_NP18-287_PUT_5"   
## [399] "AA_ASAP123_ctrl_NP19-218_AMY_5"   "AA87_ASAP76_ctrl_NP18-159_PUT_5" 
## [401] "AA_ASAP102_PD_NP21-208_SN_5"      "DA433_ASAP5_ctrl_NP16-161_SN_5"  
## [403] "DA476_ASAP10_PD_NP16-25_PFC_5"    "AA_ASAP82_PD_NP21-217_PFC_5"     
## [405] "AA_ASAP85_NP18-46_ctrl_PFC_5"     "AA_ASAP98_ctrl_NP16-119_PUT_5"   
## [407] "AA_ASAP129_ctrl_NP22-37_SN_5"     "DA473_ASAP38_PD_NP19-23_SN_5"    
## [409] "AA79_ASAP64_PD_NP16-162_PUT_5"    "AA78_ASAP63_PD_NP16-160_PUT_5"   
## [411] "AA_ASAP146_PD_NP21-04_PUT_5"      "AA_ASAP139_PD_NP17-232_PUT_5"    
## [413] "AA_ASAP138_PD_NP16-285_PUT_5"     "AA_ASAP92_ctrl_NP16-284_PUT_5"   
## [415] "DA799_ASAP19_PD_NP16-160_PFC_5"   "DA432_ASAP12_PD_P74_PFC_5"       
## [417] "DA490_ASAP11_PD_P73_PFC_5"        "DA430_ASAP9_PD_NP16-162_PFC_5"   
## [419] "DA813_ASAP17_PD_NP16-140_PFC_5"   "ASAP155_ctrl_NP23-21_PFC_5"      
## [421] "AA_ASAP154_ctrl_NP21-04_PFC_5"    "DA480_ASAP15_ctrl_NP16-21_PFC_5" 
## [423] "MJ_ASAP14_ctrl_NP16-164_PFC_5"    "AA_ASAP91_ctrl_NP17-20_PFC_5"    
## [425] "AA_ASAP89_ctrl_NP16-284_PFC_5"    "AA_ASAP84_NP17-216_ctrl_PFC_5"   
## [427] "AA_ASAP83_NP16-119_ctrl_PFC_5"    "AA_ASAP109_PD_NP21-217_AMY_5"    
## [429] "AA_ASAP115_PD_NP21-208_AMY_5"     "DA811_ASAP18_PD_NP16-140_AMY_5"  
## [431] "DA778_ASAP31_PD_NP18-117_AMY_5"   "AA_ASAP131_PD_NP23-21_AMY_5"     
## [433] "AA_ASAP128_PD_NP21-04_AMY_5"      "AA_ASAP126_PD_NP19-137_AMY_5"    
## [435] "AA_ASAP121_PD_NP17-232_AMY_5"     "AA_ASAP110_ctrl_NP16-119_AMY_5"  
## [437] "DA803_ASAP48_ctrl_NP17-256_AMY_5" "AA_ASAP99_ctrl_NP16-284_SN_5"    
## [439] "AA_ASAP137_PD_NP23-21_SN_5"       "AA_ASAP93_ctrl_NP16-293_PUT_5"   
## [441] "AA_ASAP150_PD_NP16-285_PFC_5"     "DA802_ASAP40_PD_NP19-23_AMY_5"   
## [443] "AA_ASAP96_ctrl_NP18-46_PUT_5"     "DA499_ASAP44_PD_NP19-255_PFC_5"  
## [445] "AA_ASAP147_ctrl_NP22-37_PFC_5"    "AA_ASAP88_PD_NP21-217_PUT_5"     
## [447] "DA800_ASAP20_PD_NP16-160_AMY_5"   "AA85_ASAP72_PD_NP19-23_PUT_5"    
## [449] "DA777_ASAP28_PD_NP17-191_PFC_5"   "AA_ASAP136_PD_NP21-04_SN_5"      
## [451] "AA_ASAP124_ctrl_NP22-37_AMY_5"    "AA76_ASAP74_PD_NP19-255_PUT_5"   
## [453] "DA815_ASAP37_PD_NP19-16_AMY_5"    "ASAP122_PD_NP19-91_AMY_5"        
## [455] "AA74_ASAP62_PD_NP16-140_PUT_5"    "AA_ASAP118_PD_NP22-55_SN_5"      
## [457] "AA_ASAP149_PD_NP23-21_PUT_5"      "DA782_ASAP41_PD_NP19-108_SN_5"   
## [459] "AA_ASAP151_PD_NP17-232_PFC_5"     "AA_ASAP113_ctrl_NP18-148_AMY_5"  
## [461] "DA487_ASAP8_ctrl_PT231_SN_5"      "DA808_ASAP41_PD_NP19-108_PFC_5"  
## [463] "AA_ASAP104_ctrl_NP16-119_SN_5"    "DA780_ASAP37_PD_NP19-16_AMY_5"   
## [465] "DA784_ASAP46_ctrl_NP17-256_SN_5"  "AA82_ASAP68_PD_NP18-117_PUT_5"   
## [467] "AA_ASAP101_PD_NP21-57_SN_5"       "DA809_ASAP30_PD_NP18-117_PFC_5"  
## [469] "DA511_ASAP21_PD_NP16-269_SN_5"    "AA_ASAP116_PD_NP22-55_PFC_5"     
## [471] "DA804_ASAP49_ctrl_NP18-159_PFC_5" "DA795_ASAP55_ctrl_NP19-37_PFC_5" 
## [473] "AA_ASAP141_ctrl_NP19-218_PUT_5"   "AA_ASAP127_ctrl_NP19-218_SN_5"   
## [475] "AA_ASAP144_PD_NP19-137_PUT_5"     "AA71_ASAP70_PD_NP18-304_PUT_5"   
## [477] "DA793_ASAP53_ctrl_NP19-36_AMY_5"  "DA785_ASAP47_ctrl_NP17-256_PFC_5"
## [479] "AA_ASAP152_PD_NP19-91_PFC_5"      "DA810_ASAP34_PD_NP18-304_PFC_5"  
## [481] "DA806_ASAP58_ctrl_NP19-45_PFC_5"  "DA807_ASAP29_PD_NP17-191_AMY_5"  
## [483] "AA_ASAP135_PD_NP19-137_SN_5"      "DA792_ASAP51_ctrl_NP19-36_SN_5"  
## [485] "AA_ASAP140_PD_NP19-91_PUT_5"      "DA794_ASAP54_ctrl_NP19-37_SN_5"  
## [487] "DA796_ASAP57_ctrl_NP19-45_SN_5"   "AA_ASAP133_PD_NP17-232_SN_5"     
## [489] "AA_ASAP145_ctrl_NP19-218_PFC_5"   "DA805_ASAP56_ctrl_NP19-37_AMY_5" 
## [491] "AA_ASAP87_PD_NP21-208_PUT_5"      "DA475_ASAP2_PD_NP16-25_SN_5"     
## [493] "AA84_ASAP71_PD_NP19-16_PUT_5"     "AA_ASAP100_ctrl_NP18-148_PUT_5"  
## [495] "DA509_ASAP36_PD_NP19-16_PFC_5"    "AA86_ASAP73_PD_NP19-108_PUT_5"   
## [497] "AA_ASAP94_ctrl_NP17-20_PUT_5"     "DA488_ASAP16_ctrl_PT231_PFC_5"   
## [499] "AA_ASAP114_PD_NP21-57_AMY_5"      "DA489_ASAP3_PD_P73_SN_5"         
## [501] "AA_ASAP80_PD_NP21-57_PFC_5"       "AA_ASAP97_PD_NP21-57_PUT_5"      
## [503] "DA512_ASAP60_ctrl_NP19-45_AMY_5"  "DA428_ASAP13_ctrl_NP16-161_PFC_5"
## [505] "AA_ASAP134_PD_NP19-91_SN_5"       "AA73_ASAP65_PD_NP16-269_PUT_5"   
## [507] "AA_ASAP108_ctrl_NP18-148_SN_5"    "AA_ASAP105_ctrl_NP16-293_SN_5"   
## [509] "AA_ASAP103_PD_NP21-217_SN_5"      "AA77_ASAP61_PD_NP16-25_PUT_5"    
## [511] "AA81_ASAP67_PD_NP17-191_PUT_5"    "DA814_ASAP35_PD_NP18-304_AMY_5"  
## [513] "DA431_ASAP4_PD_P74_SN_5"          "DA791_ASAP50_ctrl_NP18-159_AMY_4"
## [515] "AA_ASAP83_NP16-119_ctrl_PFC_4"    "DA811_ASAP18_PD_NP16-140_AMY_4"  
## [517] "AA_ASAP118_PD_NP22-55_SN_4"       "AA_ASAP108_ctrl_NP18-148_SN_4"   
## [519] "AA83_ASAP69_PD_NP18-287_PUT_4"    "AA_ASAP113_ctrl_NP18-148_AMY_4"  
## [521] "DA430_ASAP9_PD_NP16-162_PFC_4"    "DA429_ASAP1_PD_NP16-162_SN_4"    
## [523] "AA_ASAP110_ctrl_NP16-119_AMY_4"   "AA_ASAP97_PD_NP21-57_PUT_4"      
## [525] "DA793_ASAP53_ctrl_NP19-36_AMY_4"  "AA_ASAP112_ctrl_NP16-293_AMY_4"  
## [527] "DA805_ASAP56_ctrl_NP19-37_AMY_4"  "DA512_ASAP60_ctrl_NP19-45_AMY_4" 
## [529] "AA_ASAP126_PD_NP19-137_AMY_4"     "AA_ASAP131_PD_NP23-21_AMY_4"     
## [531] "DA783_ASAP45_PD_NP19-255_AMY_4"   "DA807_ASAP29_PD_NP17-191_AMY_4"  
## [533] "AA_ASAP115_PD_NP21-208_AMY_4"     "AA_ASAP119_PD_NP22-55_AMY_4"     
## [535] "DA474_ASAP24_PD_NP16-25_AMY_4"    "DA802_ASAP40_PD_NP19-23_AMY_4"   
## [537] "AA_ASAP86_NP18-148_ctrl_PFC_4"    "AA_ASAP145_ctrl_NP19-218_PFC_4"  
## [539] "DA795_ASAP55_ctrl_NP19-37_PFC_4"  "DA806_ASAP58_ctrl_NP19-45_PFC_4" 
## [541] "AA_ASAP89_ctrl_NP16-284_PFC_4"    "AA_ASAP90_ctrl_NP16-293_PFC_4"   
## [543] "MJ_ASAP14_ctrl_NP16-164_PFC_4"    "DA480_ASAP15_ctrl_NP16-21_PFC_4" 
## [545] "DA488_ASAP16_ctrl_PT231_PFC_4"    "DA804_ASAP49_ctrl_NP18-159_PFC_4"
## [547] "AA_ASAP151_PD_NP17-232_PFC_4"     "AA_ASAP152_PD_NP19-91_PFC_4"     
## [549] "ASAP155_ctrl_NP23-21_PFC_4"       "DA775_ASAP22_PD_NP16-269_PFC_4"  
## [551] "DA808_ASAP41_PD_NP19-108_PFC_4"   "AA_ASAP116_PD_NP22-55_PFC_4"     
## [553] "AA_ASAP80_PD_NP21-57_PFC_4"       "AA_ASAP82_PD_NP21-217_PFC_4"     
## [555] "DA476_ASAP10_PD_NP16-25_PFC_4"    "DA490_ASAP11_PD_P73_PFC_4"       
## [557] "DA432_ASAP12_PD_P74_PFC_4"        "AA_ASAP141_ctrl_NP19-218_PUT_4"  
## [559] "AA89_ASAP78_ctrl_NP19-37_PUT_4"   "AA_ASAP94_ctrl_NP17-20_PUT_4"    
## [561] "AA_ASAP96_ctrl_NP18-46_PUT_4"     "AA_ASAP100_ctrl_NP18-148_PUT_4"  
## [563] "AA_ASAP138_PD_NP16-285_PUT_4"     "AA_ASAP140_PD_NP19-91_PUT_4"     
## [565] "AA_ASAP144_PD_NP19-137_PUT_4"     "AA81_ASAP67_PD_NP17-191_PUT_4"   
## [567] "AA84_ASAP71_PD_NP19-16_PUT_4"     "AA85_ASAP72_PD_NP19-23_PUT_4"    
## [569] "AA_ASAP117_PD_NP22-55_PUT_4"      "AA_ASAP87_PD_NP21-208_PUT_4"     
## [571] "AA_ASAP88_PD_NP21-217_PUT_4"      "AA79_ASAP64_PD_NP16-162_PUT_4"   
## [573] "AA77_ASAP61_PD_NP16-25_PUT_4"     "AA73_ASAP65_PD_NP16-269_PUT_4"   
## [575] "AA71_ASAP70_PD_NP18-304_PUT_4"    "AA76_ASAP74_PD_NP19-255_PUT_4"   
## [577] "AA_ASAP127_ctrl_NP19-218_SN_4"    "DA792_ASAP51_ctrl_NP19-36_SN_4"  
## [579] "DA794_ASAP54_ctrl_NP19-37_SN_4"   "AA_ASAP104_ctrl_NP16-119_SN_4"   
## [581] "DA433_ASAP5_ctrl_NP16-161_SN_4"   "DA487_ASAP8_ctrl_PT231_SN_4"     
## [583] "AA_ASAP137_PD_NP23-21_SN_4"       "AA_ASAP101_PD_NP21-57_SN_4"      
## [585] "AA_ASAP102_PD_NP21-208_SN_4"      "DA431_ASAP4_PD_P74_SN_4"         
## [587] "DA511_ASAP21_PD_NP16-269_SN_4"    "DA473_ASAP38_PD_NP19-23_SN_4"    
## [589] "AA_ASAP114_PD_NP21-57_AMY_4"      "AA_ASAP129_ctrl_NP22-37_SN_4"    
## [591] "AA_ASAP123_ctrl_NP19-218_AMY_4"   "AA_ASAP135_PD_NP19-137_SN_4"     
## [593] "DA489_ASAP3_PD_P73_SN_4"          "AA87_ASAP76_ctrl_NP18-159_PUT_4" 
## [595] "MJ_ASAP6_ctrl_NP16-164_SN_4"      "DA778_ASAP31_PD_NP18-117_AMY_4"  
## [597] "AA_ASAP134_PD_NP19-91_SN_4"       "DA499_ASAP44_PD_NP19-255_PFC_4"  
## [599] "DA428_ASAP13_ctrl_NP16-161_PFC_4" "AA_ASAP103_PD_NP21-217_SN_4"     
## [601] "AA_ASAP98_ctrl_NP16-119_PUT_4"    "DA801_ASAP53_ctrl_NP19-36_AMY_4" 
## [603] "AA74_ASAP62_PD_NP16-140_PUT_4"    "DA475_ASAP2_PD_NP16-25_SN_4"     
## [605] "AA_ASAP133_PD_NP17-232_SN_4"      "DA782_ASAP41_PD_NP19-108_SN_4"   
## [607] "AA_ASAP89_ctrl_NP16-284_PFC_6"    "AA_ASAP123_ctrl_NP19-218_AMY_6"  
## [609] "DA428_ASAP13_ctrl_NP16-161_PFC_6" "MJ_ASAP14_ctrl_NP16-164_PFC_6"   
## [611] "AA_ASAP152_PD_NP19-91_PFC_6"      "AA_ASAP137_PD_NP23-21_SN_6"      
## [613] "DA792_ASAP51_ctrl_NP19-36_SN_6"   "DA785_ASAP47_ctrl_NP17-256_PFC_6"
## [615] "AA_ASAP133_PD_NP17-232_SN_7"      "AA_ASAP108_ctrl_NP18-148_SN_7"   
## [617] "AA_ASAP137_PD_NP23-21_SN_7"      
## 
## $order_rows
## [1] NA

---

I will need some of these objects for DE_TE_heatmaps.Rmd, so I’ll save them here

# Save data objects needed for DE analysis
save(TE_data, HERV_data, data_TE_annotation, file = "preprocessed_TE_data.RData")

# Save functions in a separate file
dump(
  c("read_te_counts_asap_region", "read_te_counts_asap_multiregion", 
    "cluster_cols_by_group", "cluster_rows_by_group", "asap_heatmap_snRNA"), 
  file = "TE_heatmap_functions.R"
)